Interactive Phylogenetics Module

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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'acertr',
	'common_name' => 'Acer truncatum',
	'tax_id' => '47965',
	'version' => 'v2.0'
)
$local_species = 'acertr'
$disabled = ''
$selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::_renderElement() - CORE/Cake/View/View.php, line 1224
View::element() - CORE/Cake/View/View.php, line 418
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::_renderElement() - CORE/Cake/View/View.php, line 1224
View::element() - CORE/Cake/View/View.php, line 418
include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::_renderElement() - CORE/Cake/View/View.php, line 1224
View::element() - CORE/Cake/View/View.php, line 418
include - APP/View/Analysis/custom_tree_creation.ctp, line 27
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933

Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]
Code Context
        $disabled    = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";

        $selected    = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";

        $num_hits    = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp'
$dataForView = array(
	'sidebar_info' => array(
		'gf_id' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'ach',
	'common_name' => 'Actinidia chinensis',
	'tax_id' => '3625',
	'version' => 'V3.0'
)
$local_species = 'ach'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'aar',
	'common_name' => 'Aethionema arabicum',
	'tax_id' => '228871',
	'version' => 'v3.1'
)
$local_species = 'aar'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'atr',
	'common_name' => 'Amborella trichopoda',
	'tax_id' => '13333',
	'version' => 'JGI v1.0'
)
$local_species = 'atr'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'aly',
	'common_name' => 'Arabidopsis lyrata',
	'tax_id' => '59689',
	'version' => 'JGI v2.1'
)
$local_species = 'aly'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'ath',
	'common_name' => 'Arabidopsis thaliana',
	'tax_id' => '3702',
	'version' => 'Araport11'
)
$local_species = 'ath'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'arhy',
	'common_name' => 'Arachis hypogaea',
	'tax_id' => '3818',
	'version' => 'v1.0'
)
$local_species = 'arhy'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$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
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'bna',
	'common_name' => 'Brassica napus',
	'tax_id' => '3708',
	'version' => 'v2.0'
)
$local_species = 'bna'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'bol',
	'common_name' => 'Brassica oleracea',
	'tax_id' => '109376',
	'version' => 'v1.0'
)
$local_species = 'bol'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'bra',
	'common_name' => 'Brassica rapa',
	'tax_id' => '3711',
	'version' => 'v1.0'
)
$local_species = 'bra'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'camsi',
	'common_name' => 'Camellia sinensis var. sinensis',
	'tax_id' => '542762',
	'version' => 'CSS_ChrLev_20200506'
)
$local_species = 'camsi'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'cansat',
	'common_name' => 'Cannabis sativa',
	'tax_id' => '3483',
	'version' => 'cs10'
)
$local_species = 'cansat'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'cru',
	'common_name' => 'Capsella rubella',
	'tax_id' => '81985',
	'version' => 'JGI v1.1'
)
$local_species = 'cru'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'can',
	'common_name' => 'Capsicum annuum',
	'tax_id' => '4072',
	'version' => 'Pepper Genome v2.0'
)
$local_species = 'can'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'chi',
	'common_name' => 'Cardamine hirsuta',
	'tax_id' => '50463',
	'version' => 'v1.0'
)
$local_species = 'chi'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'cpa',
	'common_name' => 'Carica papaya',
	'tax_id' => '3649',
	'version' => 'JGI ASGPB0.4'
)
$local_species = 'cpa'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'cil',
	'common_name' => 'Carya illinoinensis',
	'tax_id' => '32201',
	'version' => 'v1.1'
)
$local_species = 'cil'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'cqu',
	'common_name' => 'Chenopodium quinoa',
	'tax_id' => '63459',
	'version' => 'KAUST v1.0'
)
$local_species = 'cqu'
$disabled = ''
$selected = ''
$num_hits = (int) 0
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'car',
	'common_name' => 'Cicer arietinum L.',
	'tax_id' => '3827',
	'version' => 'v3.0'
)
$local_species = 'car'
$disabled = ''
$selected = ''
$num_hits = (int) 0
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'cla',
	'common_name' => 'Citrullus lanatus',
	'tax_id' => '3654',
	'version' => 'WCG v2.0'
)
$local_species = 'cla'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'ccl',
	'common_name' => 'Citrus clementina',
	'tax_id' => '85681',
	'version' => 'JGI v1.0'
)
$local_species = 'ccl'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$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) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'col',
	'common_name' => 'Corchorus olitorius',
	'tax_id' => '93759',
	'version' => 'GenBank v1.0'
)
$local_species = 'col'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'cav',
	'common_name' => 'Corylus avellana',
	'tax_id' => '13451',
	'version' => 'v1.0'
)
$local_species = 'cav'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'cme',
	'common_name' => 'Cucumis melo',
	'tax_id' => '3656',
	'version' => 'Melonomics v3.6.1'
)
$local_species = 'cme'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'csa',
	'common_name' => 'Cucumis sativus L.',
	'tax_id' => '3659',
	'version' => 'v3.0'
)
$local_species = 'csa'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'dca',
	'common_name' => 'Daucus carota',
	'tax_id' => '4039',
	'version' => 'JGI v2.0'
)
$local_species = 'dca'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'din',
	'common_name' => 'Davidia involucrata',
	'tax_id' => '16924',
	'version' => 'v1.0'
)
$local_species = 'din'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'dzi',
	'common_name' => 'Durio zibethinus',
	'tax_id' => '66656',
	'version' => 'Duzib1.0'
)
$local_species = 'dzi'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'eca',
	'common_name' => 'Erigeron canadensis',
	'tax_id' => '72917',
	'version' => 'V1.0'
)
$local_species = 'eca'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'egut',
	'common_name' => 'Erythranthe guttata',
	'tax_id' => '4155',
	'version' => 'v2.0'
)
$local_species = 'egut'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'egr',
	'common_name' => 'Eucalyptus grandis',
	'tax_id' => '71139',
	'version' => 'v2.0'
)
$local_species = 'egr'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'esa',
	'common_name' => 'Eutrema salsugineum',
	'tax_id' => '72664',
	'version' => 'v1.0'
)
$local_species = 'esa'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'fve',
	'common_name' => 'Fragaria vesca',
	'tax_id' => '57918',
	'version' => 'V4.0.a2'
)
$local_species = 'fve'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'fan',
	'common_name' => 'Fragaria x ananassa',
	'tax_id' => '3747',
	'version' => 'V1.0.a1'
)
$local_species = 'fan'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'gma',
	'common_name' => 'Glycine max',
	'tax_id' => '3847',
	'version' => 'JGI Wm82.a4.v1'
)
$local_species = 'gma'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'ghi',
	'common_name' => 'Gossypium hirsutum',
	'tax_id' => '3635',
	'version' => 'v2.1'
)
$local_species = 'ghi'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'gra',
	'common_name' => 'Gossypium raimondii',
	'tax_id' => '29730',
	'version' => 'v2.1'
)
$local_species = 'gra'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'han',
	'common_name' => 'Helianthus annuus',
	'tax_id' => '4232',
	'version' => 'r1.2'
)
$local_species = 'han'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'hma',
	'common_name' => 'Hydrangea macrophylla',
	'tax_id' => '23110',
	'version' => 'v2.1'
)
$local_species = 'hma'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'lsa',
	'common_name' => 'Lactuca sativa',
	'tax_id' => '4236',
	'version' => 'v8.0'
)
$local_species = 'lsa'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'lonja',
	'common_name' => 'Lonicera japonica',
	'tax_id' => '105884',
	'version' => 'v1.0'
)
$local_species = 'lonja'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'lja',
	'common_name' => 'Lotus japonicus',
	'tax_id' => '34305',
	'version' => 'Lj1.0v1'
)
$local_species = 'lja'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'lal',
	'common_name' => 'Lupinus albus',
	'tax_id' => '3870',
	'version' => 'v1.0'
)
$local_species = 'lal'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'mbi',
	'common_name' => 'Magnolia biondii',
	'tax_id' => '86725',
	'version' => 'v1.0'
)
$local_species = 'mbi'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'mdo',
	'common_name' => 'Malus domestica',
	'tax_id' => '3750',
	'version' => 'GDDH13 v1.1'
)
$local_species = 'mdo'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'mes',
	'common_name' => 'Manihot esculenta',
	'tax_id' => '3983',
	'version' => 'v8.1'
)
$local_species = 'mes'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'nnu',
	'common_name' => 'Nelumbo nucifera',
	'tax_id' => '4432',
	'version' => 'v2.0'
)
$local_species = 'nnu'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'nta',
	'common_name' => 'Nicotiana tabacum',
	'tax_id' => '4097',
	'version' => 'Edwards2017'
)
$local_species = 'nta'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'oeu',
	'common_name' => 'Olea europaea',
	'tax_id' => '4146',
	'version' => 'v1.0'
)
$local_species = 'oeu'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'osa',
	'common_name' => 'Oryza sativa ssp. japonica',
	'tax_id' => '39947',
	'version' => 'IRGSP-1.0-2021-05-10'
)
$local_species = 'osa'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'pso',
	'common_name' => 'Papaver somniferum',
	'tax_id' => '3469',
	'version' => 'ASM357369v1'
)
$local_species = 'pso'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'pax',
	'common_name' => 'Petunia axillaris',
	'tax_id' => '33119',
	'version' => 'Sol Genomics v1.6.2'
)
$local_species = 'pax'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'pvu',
	'common_name' => 'Phaseolus vulgaris',
	'tax_id' => '3885',
	'version' => 'v2.1'
)
$local_species = 'pvu'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'psa',
	'common_name' => 'Pisum sativum',
	'tax_id' => '3888',
	'version' => 'V1.0a'
)
$local_species = 'psa'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'ptr',
	'common_name' => 'Populus trichocarpa',
	'tax_id' => '3694',
	'version' => 'JGI v4.1'
)
$local_species = 'ptr'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'ppe',
	'common_name' => 'Prunus persica',
	'tax_id' => '3760',
	'version' => 'v2.1'
)
$local_species = 'ppe'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'pgr',
	'common_name' => 'Punica granatum',
	'tax_id' => '22663',
	'version' => 'ASM765513v2'
)
$local_species = 'pgr'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'qlo',
	'common_name' => 'Quercus lobata',
	'tax_id' => '97700',
	'version' => 'v3.0'
)
$local_species = 'qlo'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'rsi',
	'common_name' => 'Rhododendron simsii',
	'tax_id' => '118357',
	'version' => 'v1.0'
)
$local_species = 'rsi'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'rch',
	'common_name' => 'Rosa chinensis',
	'tax_id' => '74649',
	'version' => 'v2.0'
)
$local_species = 'rch'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'sbr',
	'common_name' => 'Salix brachista',
	'tax_id' => '2182728',
	'version' => 'v1.0'
)
$local_species = 'sbr'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'spa',
	'common_name' => 'Schrenkiella parvula',
	'tax_id' => '98039',
	'version' => 'v2.2'
)
$local_species = 'spa'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'sed',
	'common_name' => 'Sechium edule',
	'tax_id' => '184140',
	'version' => 'v1.0'
)
$local_species = 'sed'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'sun',
	'common_name' => 'Selenicereus undatus',
	'tax_id' => '176265',
	'version' => 'v1.0'
)
$local_species = 'sun'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'sgi',
	'common_name' => 'Sequoiadendron giganteum',
	'tax_id' => '99814',
	'version' => 'V2.0'
)
$local_species = 'sgi'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'sci',
	'common_name' => 'Simmondsia chinensis',
	'tax_id' => '3999',
	'version' => 'sc1'
)
$local_species = 'sci'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'sly',
	'common_name' => 'Solanum lycopersicum',
	'tax_id' => '4081',
	'version' => 'ITAG4.0'
)
$local_species = 'sly'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'spe',
	'common_name' => 'Solanum pennellii',
	'tax_id' => '28526',
	'version' => 'V2.0'
)
$local_species = 'spe'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'stu',
	'common_name' => 'Solanum tuberosum',
	'tax_id' => '4113',
	'version' => 'JGI v4.03'
)
$local_species = 'stu'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
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		'id' => 'HOM05D004463'
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	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
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$sidebar_info = array(
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	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'sas',
	'common_name' => 'Striga asiatica',
	'tax_id' => '4170',
	'version' => 'v2.02'
)
$local_species = 'sas'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'tha',
	'common_name' => 'Tarenaya hassleriana',
	'tax_id' => '28532',
	'version' => 'RefSeq v1'
)
$local_species = 'tha'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'tca',
	'common_name' => 'Theobroma cacao',
	'tax_id' => '3641',
	'version' => 'V2.1'
)
$local_species = 'tca'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'tpr',
	'common_name' => 'Trifolium pratense',
	'tax_id' => '57577',
	'version' => 'V2.0'
)
$local_species = 'tpr'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'twi',
	'common_name' => 'Tripterygium wilfordii',
	'tax_id' => '458696',
	'version' => 'ASM1340144v1'
)
$local_species = 'twi'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'tar',
	'common_name' => 'Trochodendron aralioides',
	'tax_id' => '4407',
	'version' => 'v1.0'
)
$local_species = 'tar'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'vma',
	'common_name' => 'Vaccinium macrocarpon',
	'tax_id' => '13750',
	'version' => 'V1.0'
)
$local_species = 'vma'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'vpl',
	'common_name' => 'Vanilla planifolia',
	'tax_id' => '51239',
	'version' => 'Elo Vpla-A Principal v1.0'
)
$local_species = 'vpl'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'vvi',
	'common_name' => 'Vitis vinifera',
	'tax_id' => '29760',
	'version' => 'Genoscope.12x'
)
$local_species = 'vvi'
$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' => 'HOM05D004463',
		'msa_exists' => array(
			'full' => true,
			'edited' => true
		),
		'tree_exists' => true,
		'num_genes' => '161',
		'num_species' => '82'
	),
	'sidebar' => 'gene_family_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'gf_genes' => array(
		'A06p48750' => 'bna',
		'A07p41130' => 'bna',
		'Aa31LG4G5800' => 'aar',
		'Actinidia00571' => 'ach',
		'AL2G35540' => 'aly',
		'AL7G10930' => 'aly',
		'Aqoxy4G02979' => 'aox',
		'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
		'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
		'AT1G75560' => 'ath',
		'ATR0998G002' => 'atr',
		'Atru.chr13.360' => 'acertr',
		'Atru.chr5.3137' => 'acertr',
		'AUR62010398' => 'cqu',
		'AUR62014431' => 'cqu',
		'AUR62016820' => 'cqu',
		'AUR62034566' => 'cqu',
		'BolC6t39994H' => 'bol',
		'BolC7t46753H' => 'bol',
		'BraA06t27741Z' => 'bra',
		'C06p49550' => 'bna',
		'C07p63410' => 'bna',
		'CAN.G95.2' => 'can',
		'CANSAT11G2458' => 'cansat',
		'CARHR068960' => 'chi',
		'CARHR247750' => 'chi',
		'Carub.0002s2242' => 'cru',
		'Ca_15338_v3' => 'car',
		'Cc02_g16980' => 'ccan',
		'Ciclev10002195m.g' => 'ccl',
		'Ciclev10029089m.g' => 'ccl',
		'CiPaw.06G128800' => 'cil',
		'CiPaw.13G045000' => 'cil',
		'CiPaw.14G035900' => 'cil',
		'ClCG02G004610' => 'cla',
		'COL.COLO4_14964' => 'col',
		'COL.COLO4_26036' => 'col',
		'Cpa.g.sc150.22' => 'cpa',
		'CsaV3_7G000350' => 'csa',
		'CSS0016875' => 'camsi',
		'CSS0035906' => 'camsi',
		'DCAR_022913' => 'dca',
		'Dinv23459' => 'din',
		'Dinv25993' => 'din',
		'Dinv39485' => 'din',
		'Dinv42004' => 'din',
		'Duzib052G0336' => 'dzi',
		'Duzib106G1221' => 'dzi',
		'Duzib132G0628' => 'dzi',
		'Duzib248G1389' => 'dzi',
		'ECA232G1454' => 'eca',
		'EL10Ac1g00556' => 'bvu',
		'Eucgr.I01324' => 'egr',
		'FAN01G1741' => 'fan',
		'FAN03G3339' => 'fan',
		'FAN06G0682' => 'fan',
		'FAN06G1248' => 'fan',
		'FAN10G2262' => 'fan',
		'FAN15G3389' => 'fan',
		'FAN20G1990' => 'fan',
		'FAN24G1814' => 'fan',
		'FAN27G0878' => 'fan',
		'FvH4_2g10323' => 'fve',
		'FvH4_7g21972' => 'fve',
		'Glyma.04G008700' => 'gma',
		'Glyma.06G008500' => 'gma',
		'Gohir.A03G199000' => 'ghi',
		'Gohir.D02G220400' => 'ghi',
		'Gohir.D10G224732' => 'ghi',
		'Gorai.005G248300' => 'gra',
		'Gorai.011G255700' => 'gra',
		'GSVIVG01009823001' => 'vvi',
		'GSVIVG01016581001' => 'vvi',
		'GSVIVG01024180001' => 'vvi',
		'HanXRQChr05g0143421' => 'han',
		'Haze_03437' => 'cav',
		'Hma1.2p1_0066F.1_g035800' => 'hma',
		'Hma1.2p1_0067F.1_g037090' => 'hma',
		'Hma1.2p1_0727F.1_g209210' => 'hma',
		'HPP92_007058' => 'vpl',
		'HPP92_007060' => 'vpl',
		'Hund00218' => 'sun',
		'Hund26868' => 'sun',
		'Lalb_Chr23g0265191' => 'lal',
		'Lj1g0018700' => 'lja',
		'Lj7P673T50' => 'lonja',
		'Lj8C86T7' => 'lonja',
		'Lj9P382T32' => 'lonja',
		'Lsat_1_v5_gn_8_16561' => 'lsa',
		'Manes.05G152600' => 'mes',
		'Manes.10G032800' => 'mes',
		'Manes.15G189900' => 'mes',
		'Manes.17G001400' => 'mes',
		'MBI19_g03564_MAGBIO' => 'mbi',
		'MD00G1040200' => 'mdo',
		'MD01G1124300' => 'mdo',
		'MD10G1063900' => 'mdo',
		'MELO3C013423.2' => 'cme',
		'Migut.B00180' => 'egut',
		'Nitab4.5_0001317g0040' => 'nta',
		'Nitab4.5_0001370g0080' => 'nta',
		'Nn5g29212' => 'nnu',
		'Nn6g32238' => 'nnu',
		'Oeu036635.1' => 'oeu',
		'Oeu046135.1' => 'oeu',
		'Oeu055628.1' => 'oeu',
		'Os03g0820700' => 'osa',
		'Os10g0545300' => 'osa',
		'Peaxi162Scf00538g00125' => 'pax',
		'Peaxi162Scf00684g00132' => 'pax',
		'PGR042G1049' => 'pgr',
		'PGR044G0901' => 'pgr',
		'PGSC0003DMG400026665' => 'stu',
		'Phvul.009G003600' => 'pvu',
		'Potri.004G161800' => 'ptr',
		'Potri.005G234700' => 'ptr',
		'Prupe.2G231800' => 'ppe',
		'Prupe.8G085500' => 'ppe',
		'Psat5g004400' => 'psa',
		'Psat5g004520' => 'psa',
		'Psat5g004560' => 'psa',
		'PSO339G4128' => 'pso',
		'PSO339G5998' => 'pso',
		'PSO384G1624' => 'pso',
		'PSO648G0094' => 'pso',
		'QL08p059074' => 'qlo',
		'QL11p046341' => 'qlo',
		'RcHm_v2.0_Chr1g0366331' => 'rch',
		'RcHm_v2.0_Chr6g0267601' => 'rch',
		'Rhsim05G0068600' => 'rsi',
		'Rhsim09G0164600' => 'rsi',
		'Sabra04G0108800' => 'sbr',
		'Sabra05G0180900' => 'sbr',
		'Sc19g0006390' => 'sci',
		'Sc20g0004810' => 'sci',
		'Sc25g0002840' => 'sci',
		'Sed0016215' => 'sed',
		'Sed0022229' => 'sed',
		'SEGI_31170' => 'sgi',
		'SGA_v2.0_scaffold326G48748' => 'sas',
		'Solyc10g054330.3' => 'sly',
		'Sopen10g024240' => 'spe',
		'Sp5g30690' => 'spa',
		'TAR369G0673' => 'tar',
		'TAR636G2492' => 'tar',
		'THA.LOC104804116' => 'tha',
		'THA.LOC104807766' => 'tha',
		'THA.LOC104809337' => 'tha',
		'THA.LOC104813804' => 'tha',
		'Thecc.02G075900' => 'tca',
		'Thecc.08G037600' => 'tca',
		'Thecc.10G047100' => 'tca',
		'Thhalv10019006m.g' => 'esa',
		'TPR.G32170' => 'tpr',
		'TPR.G32219' => 'tpr',
		'TWI31G1301' => 'twi',
		'TWI36G1578' => 'twi',
		'TWI75G1243' => 'twi',
		'vmacro23491' => 'vma',
		'Zm00001eb022680' => 'zma',
		'Zm00001eb393940' => 'zma'
	),
	'gf_id' => 'HOM05D004463',
	'gf_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'gf_types_configuration' => array(
		'HOMFAM' => array(
			'order' => '1',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		),
		'ORTHOFAM' => array(
			'order' => '2',
			'show_parentless_subfamilies' => 'false',
			'show_table' => 'true',
			'show_orphan' => false
		)
	),
	'all_species' => array(
		'acertr' => array(
			'species' => 'acertr',
			'common_name' => 'Acer truncatum',
			'tax_id' => '47965',
			'version' => 'v2.0'
		),
		'ach' => array(
			'species' => 'ach',
			'common_name' => 'Actinidia chinensis',
			'tax_id' => '3625',
			'version' => 'V3.0'
		),
		'aar' => array(
			'species' => 'aar',
			'common_name' => 'Aethionema arabicum',
			'tax_id' => '228871',
			'version' => 'v3.1'
		),
		'amhyb' => array(
			'species' => 'amhyb',
			'common_name' => 'Amaranthus hybridus',
			'tax_id' => '3565',
			'version' => 'v1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'aox' => array(
			'species' => 'aox',
			'common_name' => 'Aquilegia oxysepala',
			'tax_id' => '432649',
			'version' => 'v1.0'
		),
		'aly' => array(
			'species' => 'aly',
			'common_name' => 'Arabidopsis lyrata',
			'tax_id' => '59689',
			'version' => 'JGI v2.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'arhy' => array(
			'species' => 'arhy',
			'common_name' => 'Arachis hypogaea',
			'tax_id' => '3818',
			'version' => 'v1.0'
		),
		'ama' => array(
			'species' => 'ama',
			'common_name' => 'Avicennia marina',
			'tax_id' => '82927',
			'version' => 'v1.1 20200527'
		),
		'bvu' => array(
			'species' => 'bvu',
			'common_name' => 'Beta vulgaris',
			'tax_id' => '161934',
			'version' => 'EL10_1.0'
		),
		'bca' => array(
			'species' => 'bca',
			'common_name' => 'Brassica carinata',
			'tax_id' => '52824',
			'version' => 'V1.0'
		),
		'bna' => array(
			'species' => 'bna',
			'common_name' => 'Brassica napus',
			'tax_id' => '3708',
			'version' => 'v2.0'
		),
		'bol' => array(
			'species' => 'bol',
			'common_name' => 'Brassica oleracea',
			'tax_id' => '109376',
			'version' => 'v1.0'
		),
		'bra' => array(
			'species' => 'bra',
			'common_name' => 'Brassica rapa',
			'tax_id' => '3711',
			'version' => 'v1.0'
		),
		'camsi' => array(
			'species' => 'camsi',
			'common_name' => 'Camellia sinensis var. sinensis',
			'tax_id' => '542762',
			'version' => 'CSS_ChrLev_20200506'
		),
		'cansat' => array(
			'species' => 'cansat',
			'common_name' => 'Cannabis sativa',
			'tax_id' => '3483',
			'version' => 'cs10'
		),
		'cru' => array(
			'species' => 'cru',
			'common_name' => 'Capsella rubella',
			'tax_id' => '81985',
			'version' => 'JGI v1.1'
		),
		'can' => array(
			'species' => 'can',
			'common_name' => 'Capsicum annuum',
			'tax_id' => '4072',
			'version' => 'Pepper Genome v2.0'
		),
		'chi' => array(
			'species' => 'chi',
			'common_name' => 'Cardamine hirsuta',
			'tax_id' => '50463',
			'version' => 'v1.0'
		),
		'cpa' => array(
			'species' => 'cpa',
			'common_name' => 'Carica papaya',
			'tax_id' => '3649',
			'version' => 'JGI ASGPB0.4'
		),
		'cfa' => array(
			'species' => 'cfa',
			'common_name' => 'Carpinus fangiana',
			'tax_id' => '176857',
			'version' => 'v1.0'
		),
		'cil' => array(
			'species' => 'cil',
			'common_name' => 'Carya illinoinensis',
			'tax_id' => '32201',
			'version' => 'v1.1'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cqu' => array(
			'species' => 'cqu',
			'common_name' => 'Chenopodium quinoa',
			'tax_id' => '63459',
			'version' => 'KAUST v1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'car' => array(
			'species' => 'car',
			'common_name' => 'Cicer arietinum L.',
			'tax_id' => '3827',
			'version' => 'v3.0'
		),
		'cla' => array(
			'species' => 'cla',
			'common_name' => 'Citrullus lanatus',
			'tax_id' => '3654',
			'version' => 'WCG v2.0'
		),
		'ccl' => array(
			'species' => 'ccl',
			'common_name' => 'Citrus clementina',
			'tax_id' => '85681',
			'version' => 'JGI v1.0'
		),
		'ccan' => array(
			'species' => 'ccan',
			'common_name' => 'Coffea canephora',
			'tax_id' => '49390',
			'version' => 'Coffee Genome Hub v1'
		),
		'col' => array(
			'species' => 'col',
			'common_name' => 'Corchorus olitorius',
			'tax_id' => '93759',
			'version' => 'GenBank v1.0'
		),
		'cav' => array(
			'species' => 'cav',
			'common_name' => 'Corylus avellana',
			'tax_id' => '13451',
			'version' => 'v1.0'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cucumis melo',
			'tax_id' => '3656',
			'version' => 'Melonomics v3.6.1'
		),
		'csa' => array(
			'species' => 'csa',
			'common_name' => 'Cucumis sativus L.',
			'tax_id' => '3659',
			'version' => 'v3.0'
		),
		'dca' => array(
			'species' => 'dca',
			'common_name' => 'Daucus carota',
			'tax_id' => '4039',
			'version' => 'JGI v2.0'
		),
		'din' => array(
			'species' => 'din',
			'common_name' => 'Davidia involucrata',
			'tax_id' => '16924',
			'version' => 'v1.0'
		),
		'dzi' => array(
			'species' => 'dzi',
			'common_name' => 'Durio zibethinus',
			'tax_id' => '66656',
			'version' => 'Duzib1.0'
		),
		'eca' => array(
			'species' => 'eca',
			'common_name' => 'Erigeron canadensis',
			'tax_id' => '72917',
			'version' => 'V1.0'
		),
		'egut' => array(
			'species' => 'egut',
			'common_name' => 'Erythranthe guttata',
			'tax_id' => '4155',
			'version' => 'v2.0'
		),
		'egr' => array(
			'species' => 'egr',
			'common_name' => 'Eucalyptus grandis',
			'tax_id' => '71139',
			'version' => 'v2.0'
		),
		'esa' => array(
			'species' => 'esa',
			'common_name' => 'Eutrema salsugineum',
			'tax_id' => '72664',
			'version' => 'v1.0'
		),
		'fve' => array(
			'species' => 'fve',
			'common_name' => 'Fragaria vesca',
			'tax_id' => '57918',
			'version' => 'V4.0.a2'
		),
		'fan' => array(
			'species' => 'fan',
			'common_name' => 'Fragaria x ananassa',
			'tax_id' => '3747',
			'version' => 'V1.0.a1'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'ghi' => array(
			'species' => 'ghi',
			'common_name' => 'Gossypium hirsutum',
			'tax_id' => '3635',
			'version' => 'v2.1'
		),
		'gra' => array(
			'species' => 'gra',
			'common_name' => 'Gossypium raimondii',
			'tax_id' => '29730',
			'version' => 'v2.1'
		),
		'han' => array(
			'species' => 'han',
			'common_name' => 'Helianthus annuus',
			'tax_id' => '4232',
			'version' => 'r1.2'
		),
		'hma' => array(
			'species' => 'hma',
			'common_name' => 'Hydrangea macrophylla',
			'tax_id' => '23110',
			'version' => 'v2.1'
		),
		'lsa' => array(
			'species' => 'lsa',
			'common_name' => 'Lactuca sativa',
			'tax_id' => '4236',
			'version' => 'v8.0'
		),
		'lonja' => array(
			'species' => 'lonja',
			'common_name' => 'Lonicera japonica',
			'tax_id' => '105884',
			'version' => 'v1.0'
		),
		'lja' => array(
			'species' => 'lja',
			'common_name' => 'Lotus japonicus',
			'tax_id' => '34305',
			'version' => 'Lj1.0v1'
		),
		'lal' => array(
			'species' => 'lal',
			'common_name' => 'Lupinus albus',
			'tax_id' => '3870',
			'version' => 'v1.0'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mdo' => array(
			'species' => 'mdo',
			'common_name' => 'Malus domestica',
			'tax_id' => '3750',
			'version' => 'GDDH13 v1.1'
		),
		'mes' => array(
			'species' => 'mes',
			'common_name' => 'Manihot esculenta',
			'tax_id' => '3983',
			'version' => 'v8.1'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mtr' => array(
			'species' => 'mtr',
			'common_name' => 'Medicago truncatula',
			'tax_id' => '3880',
			'version' => 'JGI Mt4.0v1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'nnu' => array(
			'species' => 'nnu',
			'common_name' => 'Nelumbo nucifera',
			'tax_id' => '4432',
			'version' => 'v2.0'
		),
		'nta' => array(
			'species' => 'nta',
			'common_name' => 'Nicotiana tabacum',
			'tax_id' => '4097',
			'version' => 'Edwards2017'
		),
		'oeu' => array(
			'species' => 'oeu',
			'common_name' => 'Olea europaea',
			'tax_id' => '4146',
			'version' => 'v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pso' => array(
			'species' => 'pso',
			'common_name' => 'Papaver somniferum',
			'tax_id' => '3469',
			'version' => 'ASM357369v1'
		),
		'pax' => array(
			'species' => 'pax',
			'common_name' => 'Petunia axillaris',
			'tax_id' => '33119',
			'version' => 'Sol Genomics v1.6.2'
		),
		'pvu' => array(
			'species' => 'pvu',
			'common_name' => 'Phaseolus vulgaris',
			'tax_id' => '3885',
			'version' => 'v2.1'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'psa' => array(
			'species' => 'psa',
			'common_name' => 'Pisum sativum',
			'tax_id' => '3888',
			'version' => 'V1.0a'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ppe' => array(
			'species' => 'ppe',
			'common_name' => 'Prunus persica',
			'tax_id' => '3760',
			'version' => 'v2.1'
		),
		'pgr' => array(
			'species' => 'pgr',
			'common_name' => 'Punica granatum',
			'tax_id' => '22663',
			'version' => 'ASM765513v2'
		),
		'qlo' => array(
			'species' => 'qlo',
			'common_name' => 'Quercus lobata',
			'tax_id' => '97700',
			'version' => 'v3.0'
		),
		'rsi' => array(
			'species' => 'rsi',
			'common_name' => 'Rhododendron simsii',
			'tax_id' => '118357',
			'version' => 'v1.0'
		),
		'rch' => array(
			'species' => 'rch',
			'common_name' => 'Rosa chinensis',
			'tax_id' => '74649',
			'version' => 'v2.0'
		),
		'sbr' => array(
			'species' => 'sbr',
			'common_name' => 'Salix brachista',
			'tax_id' => '2182728',
			'version' => 'v1.0'
		),
		'sbo' => array(
			'species' => 'sbo',
			'common_name' => 'Salvia bowleyana',
			'tax_id' => '424416',
			'version' => 'v1.0'
		),
		'shi' => array(
			'species' => 'shi',
			'common_name' => 'Sapria himalayana',
			'tax_id' => '289637',
			'version' => 'v1.0'
		),
		'spa' => array(
			'species' => 'spa',
			'common_name' => 'Schrenkiella parvula',
			'tax_id' => '98039',
			'version' => 'v2.2'
		),
		'sed' => array(
			'species' => 'sed',
			'common_name' => 'Sechium edule',
			'tax_id' => '184140',
			'version' => 'v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sun' => array(
			'species' => 'sun',
			'common_name' => 'Selenicereus undatus',
			'tax_id' => '176265',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sci' => array(
			'species' => 'sci',
			'common_name' => 'Simmondsia chinensis',
			'tax_id' => '3999',
			'version' => 'sc1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'spe' => array(
			'species' => 'spe',
			'common_name' => 'Solanum pennellii',
			'tax_id' => '28526',
			'version' => 'V2.0'
		),
		'stu' => array(
			'species' => 'stu',
			'common_name' => 'Solanum tuberosum',
			'tax_id' => '4113',
			'version' => 'JGI v4.03'
		),
		'sas' => array(
			'species' => 'sas',
			'common_name' => 'Striga asiatica',
			'tax_id' => '4170',
			'version' => 'v2.02'
		),
		'tha' => array(
			'species' => 'tha',
			'common_name' => 'Tarenaya hassleriana',
			'tax_id' => '28532',
			'version' => 'RefSeq v1'
		),
		'tca' => array(
			'species' => 'tca',
			'common_name' => 'Theobroma cacao',
			'tax_id' => '3641',
			'version' => 'V2.1'
		),
		'tpr' => array(
			'species' => 'tpr',
			'common_name' => 'Trifolium pratense',
			'tax_id' => '57577',
			'version' => 'V2.0'
		),
		'twi' => array(
			'species' => 'twi',
			'common_name' => 'Tripterygium wilfordii',
			'tax_id' => '458696',
			'version' => 'ASM1340144v1'
		),
		'tar' => array(
			'species' => 'tar',
			'common_name' => 'Trochodendron aralioides',
			'tax_id' => '4407',
			'version' => 'v1.0'
		),
		'ugi' => array(
			'species' => 'ugi',
			'common_name' => 'Utricularia gibba',
			'tax_id' => '13748',
			'version' => 'v1.1F'
		),
		'vma' => array(
			'species' => 'vma',
			'common_name' => 'Vaccinium macrocarpon',
			'tax_id' => '13750',
			'version' => 'V1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'vmu' => array(
			'species' => 'vmu',
			'common_name' => 'Vigna mungo',
			'tax_id' => '3915',
			'version' => 'ASM1342719v1'
		),
		'vvi' => array(
			'species' => 'vvi',
			'common_name' => 'Vitis vinifera',
			'tax_id' => '29760',
			'version' => 'Genoscope.12x'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		)
	),
	'allow_async_use' => true,
	'sidebar_information' => array(
		'type' => 'gf',
		'id' => 'HOM05D004463'
	),
	'data_identifier' => 'HOM05D004463',
	'data_type' => 'gf_id'
)
$sidebar_info = array(
	'gf_id' => 'HOM05D004463',
	'msa_exists' => array(
		'full' => true,
		'edited' => true
	),
	'tree_exists' => true,
	'num_genes' => '161',
	'num_species' => '82'
)
$sidebar = 'gene_family_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$gf_genes = array(
	'A06p48750' => 'bna',
	'A07p41130' => 'bna',
	'Aa31LG4G5800' => 'aar',
	'Actinidia00571' => 'ach',
	'AL2G35540' => 'aly',
	'AL7G10930' => 'aly',
	'Aqoxy4G02979' => 'aox',
	'arahy.Tifrunner.gnm1.ann1.0JY1T4' => 'arhy',
	'arahy.Tifrunner.gnm1.ann1.2L6AT5' => 'arhy',
	'AT1G75560' => 'ath',
	'ATR0998G002' => 'atr',
	'Atru.chr13.360' => 'acertr',
	'Atru.chr5.3137' => 'acertr',
	'AUR62010398' => 'cqu',
	'AUR62014431' => 'cqu',
	'AUR62016820' => 'cqu',
	'AUR62034566' => 'cqu',
	'BolC6t39994H' => 'bol',
	'BolC7t46753H' => 'bol',
	'BraA06t27741Z' => 'bra',
	'C06p49550' => 'bna',
	'C07p63410' => 'bna',
	'CAN.G95.2' => 'can',
	'CANSAT11G2458' => 'cansat',
	'CARHR068960' => 'chi',
	'CARHR247750' => 'chi',
	'Carub.0002s2242' => 'cru',
	'Ca_15338_v3' => 'car',
	'Cc02_g16980' => 'ccan',
	'Ciclev10002195m.g' => 'ccl',
	'Ciclev10029089m.g' => 'ccl',
	'CiPaw.06G128800' => 'cil',
	'CiPaw.13G045000' => 'cil',
	'CiPaw.14G035900' => 'cil',
	'ClCG02G004610' => 'cla',
	'COL.COLO4_14964' => 'col',
	'COL.COLO4_26036' => 'col',
	'Cpa.g.sc150.22' => 'cpa',
	'CsaV3_7G000350' => 'csa',
	'CSS0016875' => 'camsi',
	'CSS0035906' => 'camsi',
	'DCAR_022913' => 'dca',
	'Dinv23459' => 'din',
	'Dinv25993' => 'din',
	'Dinv39485' => 'din',
	'Dinv42004' => 'din',
	'Duzib052G0336' => 'dzi',
	'Duzib106G1221' => 'dzi',
	'Duzib132G0628' => 'dzi',
	'Duzib248G1389' => 'dzi',
	'ECA232G1454' => 'eca',
	'EL10Ac1g00556' => 'bvu',
	'Eucgr.I01324' => 'egr',
	'FAN01G1741' => 'fan',
	'FAN03G3339' => 'fan',
	'FAN06G0682' => 'fan',
	'FAN06G1248' => 'fan',
	'FAN10G2262' => 'fan',
	'FAN15G3389' => 'fan',
	'FAN20G1990' => 'fan',
	'FAN24G1814' => 'fan',
	'FAN27G0878' => 'fan',
	'FvH4_2g10323' => 'fve',
	'FvH4_7g21972' => 'fve',
	'Glyma.04G008700' => 'gma',
	'Glyma.06G008500' => 'gma',
	'Gohir.A03G199000' => 'ghi',
	'Gohir.D02G220400' => 'ghi',
	'Gohir.D10G224732' => 'ghi',
	'Gorai.005G248300' => 'gra',
	'Gorai.011G255700' => 'gra',
	'GSVIVG01009823001' => 'vvi',
	'GSVIVG01016581001' => 'vvi',
	'GSVIVG01024180001' => 'vvi',
	'HanXRQChr05g0143421' => 'han',
	'Haze_03437' => 'cav',
	'Hma1.2p1_0066F.1_g035800' => 'hma',
	'Hma1.2p1_0067F.1_g037090' => 'hma',
	'Hma1.2p1_0727F.1_g209210' => 'hma',
	'HPP92_007058' => 'vpl',
	'HPP92_007060' => 'vpl',
	'Hund00218' => 'sun',
	'Hund26868' => 'sun',
	'Lalb_Chr23g0265191' => 'lal',
	'Lj1g0018700' => 'lja',
	'Lj7P673T50' => 'lonja',
	'Lj8C86T7' => 'lonja',
	'Lj9P382T32' => 'lonja',
	'Lsat_1_v5_gn_8_16561' => 'lsa',
	'Manes.05G152600' => 'mes',
	'Manes.10G032800' => 'mes',
	'Manes.15G189900' => 'mes',
	'Manes.17G001400' => 'mes',
	'MBI19_g03564_MAGBIO' => 'mbi',
	'MD00G1040200' => 'mdo',
	'MD01G1124300' => 'mdo',
	'MD10G1063900' => 'mdo',
	'MELO3C013423.2' => 'cme',
	'Migut.B00180' => 'egut',
	'Nitab4.5_0001317g0040' => 'nta',
	'Nitab4.5_0001370g0080' => 'nta',
	'Nn5g29212' => 'nnu',
	'Nn6g32238' => 'nnu',
	'Oeu036635.1' => 'oeu',
	'Oeu046135.1' => 'oeu',
	'Oeu055628.1' => 'oeu',
	'Os03g0820700' => 'osa',
	'Os10g0545300' => 'osa',
	'Peaxi162Scf00538g00125' => 'pax',
	'Peaxi162Scf00684g00132' => 'pax',
	'PGR042G1049' => 'pgr',
	'PGR044G0901' => 'pgr',
	'PGSC0003DMG400026665' => 'stu',
	'Phvul.009G003600' => 'pvu',
	'Potri.004G161800' => 'ptr',
	'Potri.005G234700' => 'ptr',
	'Prupe.2G231800' => 'ppe',
	'Prupe.8G085500' => 'ppe',
	'Psat5g004400' => 'psa',
	'Psat5g004520' => 'psa',
	'Psat5g004560' => 'psa',
	'PSO339G4128' => 'pso',
	'PSO339G5998' => 'pso',
	'PSO384G1624' => 'pso',
	'PSO648G0094' => 'pso',
	'QL08p059074' => 'qlo',
	'QL11p046341' => 'qlo',
	'RcHm_v2.0_Chr1g0366331' => 'rch',
	'RcHm_v2.0_Chr6g0267601' => 'rch',
	'Rhsim05G0068600' => 'rsi',
	'Rhsim09G0164600' => 'rsi',
	'Sabra04G0108800' => 'sbr',
	'Sabra05G0180900' => 'sbr',
	'Sc19g0006390' => 'sci',
	'Sc20g0004810' => 'sci',
	'Sc25g0002840' => 'sci',
	'Sed0016215' => 'sed',
	'Sed0022229' => 'sed',
	'SEGI_31170' => 'sgi',
	'SGA_v2.0_scaffold326G48748' => 'sas',
	'Solyc10g054330.3' => 'sly',
	'Sopen10g024240' => 'spe',
	'Sp5g30690' => 'spa',
	'TAR369G0673' => 'tar',
	'TAR636G2492' => 'tar',
	'THA.LOC104804116' => 'tha',
	'THA.LOC104807766' => 'tha',
	'THA.LOC104809337' => 'tha',
	'THA.LOC104813804' => 'tha',
	'Thecc.02G075900' => 'tca',
	'Thecc.08G037600' => 'tca',
	'Thecc.10G047100' => 'tca',
	'Thhalv10019006m.g' => 'esa',
	'TPR.G32170' => 'tpr',
	'TPR.G32219' => 'tpr',
	'TWI31G1301' => 'twi',
	'TWI36G1578' => 'twi',
	'TWI75G1243' => 'twi',
	'vmacro23491' => 'vma',
	'Zm00001eb022680' => 'zma',
	'Zm00001eb393940' => 'zma'
)
$gf_id = 'HOM05D004463'
$gf_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$gf_types_configuration = array(
	'HOMFAM' => array(
		'order' => '1',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	),
	'ORTHOFAM' => array(
		'order' => '2',
		'show_parentless_subfamilies' => 'false',
		'show_table' => 'true',
		'show_orphan' => false
	)
)
$all_species = array(
	'acertr' => array(
		'species' => 'acertr',
		'common_name' => 'Acer truncatum',
		'tax_id' => '47965',
		'version' => 'v2.0'
	),
	'ach' => array(
		'species' => 'ach',
		'common_name' => 'Actinidia chinensis',
		'tax_id' => '3625',
		'version' => 'V3.0'
	),
	'aar' => array(
		'species' => 'aar',
		'common_name' => 'Aethionema arabicum',
		'tax_id' => '228871',
		'version' => 'v3.1'
	),
	'amhyb' => array(
		'species' => 'amhyb',
		'common_name' => 'Amaranthus hybridus',
		'tax_id' => '3565',
		'version' => 'v1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'aox' => array(
		'species' => 'aox',
		'common_name' => 'Aquilegia oxysepala',
		'tax_id' => '432649',
		'version' => 'v1.0'
	),
	'aly' => array(
		'species' => 'aly',
		'common_name' => 'Arabidopsis lyrata',
		'tax_id' => '59689',
		'version' => 'JGI v2.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'arhy' => array(
		'species' => 'arhy',
		'common_name' => 'Arachis hypogaea',
		'tax_id' => '3818',
		'version' => 'v1.0'
	),
	'ama' => array(
		'species' => 'ama',
		'common_name' => 'Avicennia marina',
		'tax_id' => '82927',
		'version' => 'v1.1 20200527'
	),
	'bvu' => array(
		'species' => 'bvu',
		'common_name' => 'Beta vulgaris',
		'tax_id' => '161934',
		'version' => 'EL10_1.0'
	),
	'bca' => array(
		'species' => 'bca',
		'common_name' => 'Brassica carinata',
		'tax_id' => '52824',
		'version' => 'V1.0'
	),
	'bna' => array(
		'species' => 'bna',
		'common_name' => 'Brassica napus',
		'tax_id' => '3708',
		'version' => 'v2.0'
	),
	'bol' => array(
		'species' => 'bol',
		'common_name' => 'Brassica oleracea',
		'tax_id' => '109376',
		'version' => 'v1.0'
	),
	'bra' => array(
		'species' => 'bra',
		'common_name' => 'Brassica rapa',
		'tax_id' => '3711',
		'version' => 'v1.0'
	),
	'camsi' => array(
		'species' => 'camsi',
		'common_name' => 'Camellia sinensis var. sinensis',
		'tax_id' => '542762',
		'version' => 'CSS_ChrLev_20200506'
	),
	'cansat' => array(
		'species' => 'cansat',
		'common_name' => 'Cannabis sativa',
		'tax_id' => '3483',
		'version' => 'cs10'
	),
	'cru' => array(
		'species' => 'cru',
		'common_name' => 'Capsella rubella',
		'tax_id' => '81985',
		'version' => 'JGI v1.1'
	),
	'can' => array(
		'species' => 'can',
		'common_name' => 'Capsicum annuum',
		'tax_id' => '4072',
		'version' => 'Pepper Genome v2.0'
	),
	'chi' => array(
		'species' => 'chi',
		'common_name' => 'Cardamine hirsuta',
		'tax_id' => '50463',
		'version' => 'v1.0'
	),
	'cpa' => array(
		'species' => 'cpa',
		'common_name' => 'Carica papaya',
		'tax_id' => '3649',
		'version' => 'JGI ASGPB0.4'
	),
	'cfa' => array(
		'species' => 'cfa',
		'common_name' => 'Carpinus fangiana',
		'tax_id' => '176857',
		'version' => 'v1.0'
	),
	'cil' => array(
		'species' => 'cil',
		'common_name' => 'Carya illinoinensis',
		'tax_id' => '32201',
		'version' => 'v1.1'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cqu' => array(
		'species' => 'cqu',
		'common_name' => 'Chenopodium quinoa',
		'tax_id' => '63459',
		'version' => 'KAUST v1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'car' => array(
		'species' => 'car',
		'common_name' => 'Cicer arietinum L.',
		'tax_id' => '3827',
		'version' => 'v3.0'
	),
	'cla' => array(
		'species' => 'cla',
		'common_name' => 'Citrullus lanatus',
		'tax_id' => '3654',
		'version' => 'WCG v2.0'
	),
	'ccl' => array(
		'species' => 'ccl',
		'common_name' => 'Citrus clementina',
		'tax_id' => '85681',
		'version' => 'JGI v1.0'
	),
	'ccan' => array(
		'species' => 'ccan',
		'common_name' => 'Coffea canephora',
		'tax_id' => '49390',
		'version' => 'Coffee Genome Hub v1'
	),
	'col' => array(
		'species' => 'col',
		'common_name' => 'Corchorus olitorius',
		'tax_id' => '93759',
		'version' => 'GenBank v1.0'
	),
	'cav' => array(
		'species' => 'cav',
		'common_name' => 'Corylus avellana',
		'tax_id' => '13451',
		'version' => 'v1.0'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cucumis melo',
		'tax_id' => '3656',
		'version' => 'Melonomics v3.6.1'
	),
	'csa' => array(
		'species' => 'csa',
		'common_name' => 'Cucumis sativus L.',
		'tax_id' => '3659',
		'version' => 'v3.0'
	),
	'dca' => array(
		'species' => 'dca',
		'common_name' => 'Daucus carota',
		'tax_id' => '4039',
		'version' => 'JGI v2.0'
	),
	'din' => array(
		'species' => 'din',
		'common_name' => 'Davidia involucrata',
		'tax_id' => '16924',
		'version' => 'v1.0'
	),
	'dzi' => array(
		'species' => 'dzi',
		'common_name' => 'Durio zibethinus',
		'tax_id' => '66656',
		'version' => 'Duzib1.0'
	),
	'eca' => array(
		'species' => 'eca',
		'common_name' => 'Erigeron canadensis',
		'tax_id' => '72917',
		'version' => 'V1.0'
	),
	'egut' => array(
		'species' => 'egut',
		'common_name' => 'Erythranthe guttata',
		'tax_id' => '4155',
		'version' => 'v2.0'
	),
	'egr' => array(
		'species' => 'egr',
		'common_name' => 'Eucalyptus grandis',
		'tax_id' => '71139',
		'version' => 'v2.0'
	),
	'esa' => array(
		'species' => 'esa',
		'common_name' => 'Eutrema salsugineum',
		'tax_id' => '72664',
		'version' => 'v1.0'
	),
	'fve' => array(
		'species' => 'fve',
		'common_name' => 'Fragaria vesca',
		'tax_id' => '57918',
		'version' => 'V4.0.a2'
	),
	'fan' => array(
		'species' => 'fan',
		'common_name' => 'Fragaria x ananassa',
		'tax_id' => '3747',
		'version' => 'V1.0.a1'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'ghi' => array(
		'species' => 'ghi',
		'common_name' => 'Gossypium hirsutum',
		'tax_id' => '3635',
		'version' => 'v2.1'
	),
	'gra' => array(
		'species' => 'gra',
		'common_name' => 'Gossypium raimondii',
		'tax_id' => '29730',
		'version' => 'v2.1'
	),
	'han' => array(
		'species' => 'han',
		'common_name' => 'Helianthus annuus',
		'tax_id' => '4232',
		'version' => 'r1.2'
	),
	'hma' => array(
		'species' => 'hma',
		'common_name' => 'Hydrangea macrophylla',
		'tax_id' => '23110',
		'version' => 'v2.1'
	),
	'lsa' => array(
		'species' => 'lsa',
		'common_name' => 'Lactuca sativa',
		'tax_id' => '4236',
		'version' => 'v8.0'
	),
	'lonja' => array(
		'species' => 'lonja',
		'common_name' => 'Lonicera japonica',
		'tax_id' => '105884',
		'version' => 'v1.0'
	),
	'lja' => array(
		'species' => 'lja',
		'common_name' => 'Lotus japonicus',
		'tax_id' => '34305',
		'version' => 'Lj1.0v1'
	),
	'lal' => array(
		'species' => 'lal',
		'common_name' => 'Lupinus albus',
		'tax_id' => '3870',
		'version' => 'v1.0'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mdo' => array(
		'species' => 'mdo',
		'common_name' => 'Malus domestica',
		'tax_id' => '3750',
		'version' => 'GDDH13 v1.1'
	),
	'mes' => array(
		'species' => 'mes',
		'common_name' => 'Manihot esculenta',
		'tax_id' => '3983',
		'version' => 'v8.1'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mtr' => array(
		'species' => 'mtr',
		'common_name' => 'Medicago truncatula',
		'tax_id' => '3880',
		'version' => 'JGI Mt4.0v1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'nnu' => array(
		'species' => 'nnu',
		'common_name' => 'Nelumbo nucifera',
		'tax_id' => '4432',
		'version' => 'v2.0'
	),
	'nta' => array(
		'species' => 'nta',
		'common_name' => 'Nicotiana tabacum',
		'tax_id' => '4097',
		'version' => 'Edwards2017'
	),
	'oeu' => array(
		'species' => 'oeu',
		'common_name' => 'Olea europaea',
		'tax_id' => '4146',
		'version' => 'v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pso' => array(
		'species' => 'pso',
		'common_name' => 'Papaver somniferum',
		'tax_id' => '3469',
		'version' => 'ASM357369v1'
	),
	'pax' => array(
		'species' => 'pax',
		'common_name' => 'Petunia axillaris',
		'tax_id' => '33119',
		'version' => 'Sol Genomics v1.6.2'
	),
	'pvu' => array(
		'species' => 'pvu',
		'common_name' => 'Phaseolus vulgaris',
		'tax_id' => '3885',
		'version' => 'v2.1'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'psa' => array(
		'species' => 'psa',
		'common_name' => 'Pisum sativum',
		'tax_id' => '3888',
		'version' => 'V1.0a'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ppe' => array(
		'species' => 'ppe',
		'common_name' => 'Prunus persica',
		'tax_id' => '3760',
		'version' => 'v2.1'
	),
	'pgr' => array(
		'species' => 'pgr',
		'common_name' => 'Punica granatum',
		'tax_id' => '22663',
		'version' => 'ASM765513v2'
	),
	'qlo' => array(
		'species' => 'qlo',
		'common_name' => 'Quercus lobata',
		'tax_id' => '97700',
		'version' => 'v3.0'
	),
	'rsi' => array(
		'species' => 'rsi',
		'common_name' => 'Rhododendron simsii',
		'tax_id' => '118357',
		'version' => 'v1.0'
	),
	'rch' => array(
		'species' => 'rch',
		'common_name' => 'Rosa chinensis',
		'tax_id' => '74649',
		'version' => 'v2.0'
	),
	'sbr' => array(
		'species' => 'sbr',
		'common_name' => 'Salix brachista',
		'tax_id' => '2182728',
		'version' => 'v1.0'
	),
	'sbo' => array(
		'species' => 'sbo',
		'common_name' => 'Salvia bowleyana',
		'tax_id' => '424416',
		'version' => 'v1.0'
	),
	'shi' => array(
		'species' => 'shi',
		'common_name' => 'Sapria himalayana',
		'tax_id' => '289637',
		'version' => 'v1.0'
	),
	'spa' => array(
		'species' => 'spa',
		'common_name' => 'Schrenkiella parvula',
		'tax_id' => '98039',
		'version' => 'v2.2'
	),
	'sed' => array(
		'species' => 'sed',
		'common_name' => 'Sechium edule',
		'tax_id' => '184140',
		'version' => 'v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sun' => array(
		'species' => 'sun',
		'common_name' => 'Selenicereus undatus',
		'tax_id' => '176265',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sci' => array(
		'species' => 'sci',
		'common_name' => 'Simmondsia chinensis',
		'tax_id' => '3999',
		'version' => 'sc1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'spe' => array(
		'species' => 'spe',
		'common_name' => 'Solanum pennellii',
		'tax_id' => '28526',
		'version' => 'V2.0'
	),
	'stu' => array(
		'species' => 'stu',
		'common_name' => 'Solanum tuberosum',
		'tax_id' => '4113',
		'version' => 'JGI v4.03'
	),
	'sas' => array(
		'species' => 'sas',
		'common_name' => 'Striga asiatica',
		'tax_id' => '4170',
		'version' => 'v2.02'
	),
	'tha' => array(
		'species' => 'tha',
		'common_name' => 'Tarenaya hassleriana',
		'tax_id' => '28532',
		'version' => 'RefSeq v1'
	),
	'tca' => array(
		'species' => 'tca',
		'common_name' => 'Theobroma cacao',
		'tax_id' => '3641',
		'version' => 'V2.1'
	),
	'tpr' => array(
		'species' => 'tpr',
		'common_name' => 'Trifolium pratense',
		'tax_id' => '57577',
		'version' => 'V2.0'
	),
	'twi' => array(
		'species' => 'twi',
		'common_name' => 'Tripterygium wilfordii',
		'tax_id' => '458696',
		'version' => 'ASM1340144v1'
	),
	'tar' => array(
		'species' => 'tar',
		'common_name' => 'Trochodendron aralioides',
		'tax_id' => '4407',
		'version' => 'v1.0'
	),
	'ugi' => array(
		'species' => 'ugi',
		'common_name' => 'Utricularia gibba',
		'tax_id' => '13748',
		'version' => 'v1.1F'
	),
	'vma' => array(
		'species' => 'vma',
		'common_name' => 'Vaccinium macrocarpon',
		'tax_id' => '13750',
		'version' => 'V1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'vmu' => array(
		'species' => 'vmu',
		'common_name' => 'Vigna mungo',
		'tax_id' => '3915',
		'version' => 'ASM1342719v1'
	),
	'vvi' => array(
		'species' => 'vvi',
		'common_name' => 'Vitis vinifera',
		'tax_id' => '29760',
		'version' => 'Genoscope.12x'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	)
)
$allow_async_use = true
$sidebar_information = array(
	'type' => 'gf',
	'id' => 'HOM05D004463'
)
$data_identifier = 'HOM05D004463'
$data_type = 'gf_id'
$species_gene_counts = array(
	'bna' => (int) 4,
	'aar' => (int) 1,
	'ach' => (int) 1,
	'aly' => (int) 2,
	'aox' => (int) 1,
	'arhy' => (int) 2,
	'ath' => (int) 1,
	'atr' => (int) 1,
	'acertr' => (int) 2,
	'cqu' => (int) 4,
	'bol' => (int) 2,
	'bra' => (int) 1,
	'can' => (int) 1,
	'cansat' => (int) 1,
	'chi' => (int) 2,
	'cru' => (int) 1,
	'car' => (int) 1,
	'ccan' => (int) 1,
	'ccl' => (int) 2,
	'cil' => (int) 3,
	'cla' => (int) 1,
	'col' => (int) 2,
	'cpa' => (int) 1,
	'csa' => (int) 1,
	'camsi' => (int) 2,
	'dca' => (int) 1,
	'din' => (int) 4,
	'dzi' => (int) 4,
	'eca' => (int) 1,
	'bvu' => (int) 1,
	'egr' => (int) 1,
	'fan' => (int) 9,
	'fve' => (int) 2,
	'gma' => (int) 2,
	'ghi' => (int) 3,
	'gra' => (int) 2,
	'vvi' => (int) 3,
	'han' => (int) 1,
	'cav' => (int) 1,
	'hma' => (int) 3,
	'vpl' => (int) 2,
	'sun' => (int) 2,
	'lal' => (int) 1,
	'lja' => (int) 1,
	'lonja' => (int) 3,
	'lsa' => (int) 1,
	'mes' => (int) 4,
	'mbi' => (int) 1,
	'mdo' => (int) 3,
	'cme' => (int) 1,
	'egut' => (int) 1,
	'nta' => (int) 2,
	'nnu' => (int) 2,
	'oeu' => (int) 3,
	'osa' => (int) 2,
	'pax' => (int) 2,
	'pgr' => (int) 2,
	'stu' => (int) 1,
	'pvu' => (int) 1,
	'ptr' => (int) 2,
	'ppe' => (int) 2,
	'psa' => (int) 3,
	'pso' => (int) 4,
	'qlo' => (int) 2,
	'rch' => (int) 2,
	'rsi' => (int) 2,
	'sbr' => (int) 2,
	'sci' => (int) 3,
	'sed' => (int) 2,
	'sgi' => (int) 1,
	'sas' => (int) 1,
	'sly' => (int) 1,
	'spe' => (int) 1,
	'spa' => (int) 1,
	'tar' => (int) 2,
	'tha' => (int) 4,
	'tca' => (int) 3,
	'esa' => (int) 1,
	'tpr' => (int) 2,
	'twi' => (int) 3,
	'vma' => (int) 1,
	'zma' => (int) 2
)
$gf_gene_species = 'zma'
$gf_gene_id = 'Zm00001eb393940'
$species_info = array(
	'species' => 'zma',
	'common_name' => 'Zea mays',
	'tax_id' => '4577',
	'version' => 'NAM v5.0'
)
$local_species = 'zma'
$disabled = ''
$selected = ''
$num_hits = (int) 1
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