Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]
Code Context
                                                    echo "<td><input type='checkbox' name='selected_genes[]' value='".$similarity_hit['gene_id']."' ".$checked." /></td>\n";
                                                    echo "<td>".$this->Html->link($similarity_hit_gene,array("controller"=>"genes","action"=>"view",$similarity_hit_gene),array("target"=>"_blank"))."</td>\n";
                                                    echo "<td>".$this->Html->link($similarity_hit['common_name'],array("controller"=>"organism","action"=>"view",urlencode($similarity_hit['common_name'])))."</td>\n";
$viewFile = '/xtras/group/biocomp/plaza/versions/plaza_pico_03/app/View/Analysis/custom_tree_creation.ctp'
$dataForView = array(
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'similarity_hits_genes' => array(
		'ENSMUSG00000023045' => array(
			'gene_id' => 'ENSMUSG00000023045',
			'e_value' => '0.0',
			'bit_score' => '1081',
			'alignment_length' => '526',
			'identity_percentage' => '100.00',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000167780' => array(
			'gene_id' => 'ENSG00000167780',
			'e_value' => '0.0',
			'bit_score' => '867',
			'alignment_length' => '528',
			'identity_percentage' => '81.63',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000057252' => array(
			'gene_id' => 'ENSG00000057252',
			'e_value' => '2e-171',
			'bit_score' => '503',
			'alignment_length' => '536',
			'identity_percentage' => '47.20',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000026600' => array(
			'gene_id' => 'ENSMUSG00000026600',
			'e_value' => '2e-169',
			'bit_score' => '498',
			'alignment_length' => '528',
			'identity_percentage' => '46.97',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0037612' => array(
			'gene_id' => 'FBgn0037612',
			'e_value' => '2e-70',
			'bit_score' => '241',
			'alignment_length' => '550',
			'identity_percentage' => '31.27',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00007174' => array(
			'gene_id' => 'WBGene00007174',
			'e_value' => '4e-70',
			'bit_score' => '238',
			'alignment_length' => '460',
			'identity_percentage' => '30.43',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte391310' => array(
			'gene_id' => 'pte391310',
			'e_value' => '1e-60',
			'bit_score' => '215',
			'alignment_length' => '493',
			'identity_percentage' => '28.19',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte347260' => array(
			'gene_id' => 'pte347260',
			'e_value' => '1e-57',
			'bit_score' => '206',
			'alignment_length' => '492',
			'identity_percentage' => '27.64',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu71270' => array(
			'gene_id' => 'gsu71270',
			'e_value' => '5e-36',
			'bit_score' => '144',
			'alignment_length' => '237',
			'identity_percentage' => '36.29',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr43280' => array(
			'gene_id' => 'ccr43280',
			'e_value' => '1e-35',
			'bit_score' => '138',
			'alignment_length' => '240',
			'identity_percentage' => '36.67',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte337520' => array(
			'gene_id' => 'pte337520',
			'e_value' => '1e-34',
			'bit_score' => '139',
			'alignment_length' => '431',
			'identity_percentage' => '27.38',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM17G01990' => array(
			'gene_id' => 'CM17G01990',
			'e_value' => '1e-33',
			'bit_score' => '138',
			'alignment_length' => '240',
			'identity_percentage' => '32.08',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0282197' => array(
			'gene_id' => 'DDB_G0282197',
			'e_value' => '4e-32',
			'bit_score' => '132',
			'alignment_length' => '240',
			'identity_percentage' => '33.33',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0271342' => array(
			'gene_id' => 'DDB_G0271342',
			'e_value' => '2e-31',
			'bit_score' => '131',
			'alignment_length' => '255',
			'identity_percentage' => '32.94',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT2G19450' => array(
			'gene_id' => 'AT2G19450',
			'e_value' => '6e-31',
			'bit_score' => '129',
			'alignment_length' => '299',
			'identity_percentage' => '30.77',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS06G36800' => array(
			'gene_id' => 'OS06G36800',
			'e_value' => '1e-30',
			'bit_score' => '128',
			'alignment_length' => '256',
			'identity_percentage' => '33.20',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM05G01000' => array(
			'gene_id' => 'CM05G01000',
			'e_value' => '2e-30',
			'bit_score' => '128',
			'alignment_length' => '382',
			'identity_percentage' => '28.01',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS05G10810' => array(
			'gene_id' => 'OS05G10810',
			'e_value' => '2e-30',
			'bit_score' => '128',
			'alignment_length' => '407',
			'identity_percentage' => '27.52',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte388530' => array(
			'gene_id' => 'pte388530',
			'e_value' => '3e-30',
			'bit_score' => '126',
			'alignment_length' => '401',
			'identity_percentage' => '27.43',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0044G00390' => array(
			'gene_id' => 'AA0044G00390',
			'e_value' => '3e-28',
			'bit_score' => '117',
			'alignment_length' => '229',
			'identity_percentage' => '33.62',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu32710' => array(
			'gene_id' => 'gsu32710',
			'e_value' => '2e-27',
			'bit_score' => '118',
			'alignment_length' => '316',
			'identity_percentage' => '29.43',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00036G00750' => array(
			'gene_id' => 'ATR_00036G00750',
			'e_value' => '3e-27',
			'bit_score' => '119',
			'alignment_length' => '235',
			'identity_percentage' => '31.91',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte324070' => array(
			'gene_id' => 'pte324070',
			'e_value' => '1e-26',
			'bit_score' => '116',
			'alignment_length' => '210',
			'identity_percentage' => '32.86',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000185000' => array(
			'gene_id' => 'ENSG00000185000',
			'e_value' => '7e-26',
			'bit_score' => '114',
			'alignment_length' => '241',
			'identity_percentage' => '31.54',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP02G02150' => array(
			'gene_id' => 'TP02G02150',
			'e_value' => '1e-25',
			'bit_score' => '112',
			'alignment_length' => '261',
			'identity_percentage' => '31.42',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr126440' => array(
			'gene_id' => 'ccr126440',
			'e_value' => '2e-25',
			'bit_score' => '107',
			'alignment_length' => '153',
			'identity_percentage' => '38.56',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr138420' => array(
			'gene_id' => 'ccr138420',
			'e_value' => '3e-25',
			'bit_score' => '106',
			'alignment_length' => '166',
			'identity_percentage' => '36.14',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte626290' => array(
			'gene_id' => 'pte626290',
			'e_value' => '6e-25',
			'bit_score' => '112',
			'alignment_length' => '246',
			'identity_percentage' => '32.93',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte535750' => array(
			'gene_id' => 'pte535750',
			'e_value' => '1e-24',
			'bit_score' => '111',
			'alignment_length' => '246',
			'identity_percentage' => '32.52',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'phs336410' => array(
			'gene_id' => 'phs336410',
			'e_value' => '4e-24',
			'bit_score' => '108',
			'alignment_length' => '271',
			'identity_percentage' => '29.52',
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0074G00140' => array(
			'gene_id' => 'ES0074G00140',
			'e_value' => '5e-24',
			'bit_score' => '107',
			'alignment_length' => '247',
			'identity_percentage' => '32.39',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_044G00040' => array(
			'gene_id' => 'CNC64A_044G00040',
			'e_value' => '2e-23',
			'bit_score' => '107',
			'alignment_length' => '319',
			'identity_percentage' => '29.15',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G01950' => array(
			'gene_id' => 'CV00G01950',
			'e_value' => '4e-23',
			'bit_score' => '106',
			'alignment_length' => '239',
			'identity_percentage' => '31.38',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu141150' => array(
			'gene_id' => 'gsu141150',
			'e_value' => '8e-23',
			'bit_score' => '105',
			'alignment_length' => '249',
			'identity_percentage' => '29.72',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.17g00460' => array(
			'gene_id' => 'RCC4223.17g00460',
			'e_value' => '1e-22',
			'bit_score' => '105',
			'alignment_length' => '247',
			'identity_percentage' => '31.98',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YNR019W' => array(
			'gene_id' => 'YNR019W',
			'e_value' => '5e-22',
			'bit_score' => '103',
			'alignment_length' => '246',
			'identity_percentage' => '31.71',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0004797' => array(
			'gene_id' => 'FBgn0004797',
			'e_value' => '1e-21',
			'bit_score' => '102',
			'alignment_length' => '235',
			'identity_percentage' => '28.94',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00066G00890' => array(
			'gene_id' => 'PP00066G00890',
			'e_value' => '3e-21',
			'bit_score' => '100',
			'alignment_length' => '240',
			'identity_percentage' => '31.67',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G00180' => array(
			'gene_id' => 'PI00G00180',
			'e_value' => '3e-21',
			'bit_score' => '101',
			'alignment_length' => '175',
			'identity_percentage' => '33.71',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G04390' => array(
			'gene_id' => 'AP00G04390',
			'e_value' => '5e-21',
			'bit_score' => '100',
			'alignment_length' => '254',
			'identity_percentage' => '30.71',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00131G00140' => array(
			'gene_id' => 'PP00131G00140',
			'e_value' => '4e-20',
			'bit_score' => '97.1',
			'alignment_length' => '134',
			'identity_percentage' => '35.82',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'SPAC13G7.05' => array(
			'gene_id' => 'SPAC13G7.05',
			'e_value' => '5e-20',
			'bit_score' => '97.4',
			'alignment_length' => '181',
			'identity_percentage' => '30.94',
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_101968g1' => array(
			'gene_id' => 'Naga_101968g1',
			'e_value' => '4e-19',
			'bit_score' => '89.0',
			'alignment_length' => '90',
			'identity_percentage' => '48.89',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC009G08820' => array(
			'gene_id' => 'FC009G08820',
			'e_value' => '1e-18',
			'bit_score' => '92.0',
			'alignment_length' => '262',
			'identity_percentage' => '30.53',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00010408' => array(
			'gene_id' => 'WBGene00010408',
			'e_value' => '2e-18',
			'bit_score' => '92.0',
			'alignment_length' => '236',
			'identity_percentage' => '29.24',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YCR048W' => array(
			'gene_id' => 'YCR048W',
			'e_value' => '2e-18',
			'bit_score' => '92.4',
			'alignment_length' => '205',
			'identity_percentage' => '32.68',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh630660' => array(
			'gene_id' => 'emh630660',
			'e_value' => '7e-17',
			'bit_score' => '83.2',
			'alignment_length' => '149',
			'identity_percentage' => '36.91',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR01G09980' => array(
			'gene_id' => 'CR01G09980',
			'e_value' => '1e-16',
			'bit_score' => '85.9',
			'alignment_length' => '164',
			'identity_percentage' => '34.15',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'SPCP1E11.05c' => array(
			'gene_id' => 'SPCP1E11.05c',
			'e_value' => '7e-16',
			'bit_score' => '84.3',
			'alignment_length' => '176',
			'identity_percentage' => '32.39',
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G95160' => array(
			'gene_id' => 'AC00G95160',
			'e_value' => '3e-15',
			'bit_score' => '82.0',
			'alignment_length' => '263',
			'identity_percentage' => '27.76',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte337540' => array(
			'gene_id' => 'pte337540',
			'e_value' => '3e-15',
			'bit_score' => '80.9',
			'alignment_length' => '262',
			'identity_percentage' => '30.53',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte374450' => array(
			'gene_id' => 'pte374450',
			'e_value' => '9e-15',
			'bit_score' => '79.7',
			'alignment_length' => '262',
			'identity_percentage' => '29.39',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G15360' => array(
			'gene_id' => 'VC00G15360',
			'e_value' => '5e-10',
			'bit_score' => '65.1',
			'alignment_length' => '250',
			'identity_percentage' => '25.20',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0276523' => array(
			'gene_id' => 'DDB_G0276523',
			'e_value' => '2e-07',
			'bit_score' => '57.4',
			'alignment_length' => '180',
			'identity_percentage' => '26.67',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte176290' => array(
			'gene_id' => 'pte176290',
			'e_value' => '1e-06',
			'bit_score' => '53.5',
			'alignment_length' => '147',
			'identity_percentage' => '26.53',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'mus' => array(
			(int) 0 => 'ENSMUSG00000023045',
			(int) 1 => 'ENSMUSG00000026600'
		),
		'hom' => array(
			(int) 0 => 'ENSG00000167780',
			(int) 1 => 'ENSG00000057252',
			(int) 2 => 'ENSG00000185000'
		),
		'drm' => array(
			(int) 0 => 'FBgn0037612',
			(int) 1 => 'FBgn0004797'
		),
		'cel' => array(
			(int) 0 => 'WBGene00007174',
			(int) 1 => 'WBGene00010408'
		),
		'pte' => array(
			(int) 0 => 'pte391310',
			(int) 1 => 'pte347260',
			(int) 2 => 'pte337520',
			(int) 3 => 'pte388530',
			(int) 4 => 'pte324070',
			(int) 5 => 'pte626290',
			(int) 6 => 'pte535750',
			(int) 7 => 'pte337540',
			(int) 8 => 'pte374450',
			(int) 9 => 'pte176290'
		),
		'gsu' => array(
			(int) 0 => 'gsu71270',
			(int) 1 => 'gsu32710',
			(int) 2 => 'gsu141150'
		),
		'ccr' => array(
			(int) 0 => 'ccr43280',
			(int) 1 => 'ccr126440',
			(int) 2 => 'ccr138420'
		),
		'cme' => array(
			(int) 0 => 'CM17G01990',
			(int) 1 => 'CM05G01000'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0282197',
			(int) 1 => 'DDB_G0271342',
			(int) 2 => 'DDB_G0276523'
		),
		'ath' => array(
			(int) 0 => 'AT2G19450'
		),
		'osa' => array(
			(int) 0 => 'OS06G36800',
			(int) 1 => 'OS05G10810'
		),
		'aan' => array(
			(int) 0 => 'AA0044G00390'
		),
		'atr' => array(
			(int) 0 => 'ATR_00036G00750'
		),
		'tps' => array(
			(int) 0 => 'TP02G02150'
		),
		'phs' => array(
			(int) 0 => 'phs336410'
		),
		'esi' => array(
			(int) 0 => 'ES0074G00140'
		),
		'cvu' => array(
			(int) 0 => 'CV00G01950'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.17g00460'
		),
		'sac' => array(
			(int) 0 => 'YNR019W',
			(int) 1 => 'YCR048W'
		),
		'ppa' => array(
			(int) 0 => 'PP00066G00890',
			(int) 1 => 'PP00131G00140'
		),
		'pse3' => array(
			(int) 0 => 'PI00G00180'
		),
		'apr' => array(
			(int) 0 => 'AP00G04390'
		),
		'scp' => array(
			(int) 0 => 'SPAC13G7.05',
			(int) 1 => 'SPCP1E11.05c'
		),
		'nga' => array(
			(int) 0 => 'Naga_101968g1'
		),
		'fcy' => array(
			(int) 0 => 'FC009G08820'
		),
		'emh' => array(
			(int) 0 => 'emh630660'
		),
		'cre' => array(
			(int) 0 => 'CR01G09980'
		),
		'acg' => array(
			(int) 0 => 'AC00G95160'
		),
		'vca' => array(
			(int) 0 => 'VC00G15360'
		)
	),
	'gene_id' => 'ENSMUSG00000023045',
	'all_species_index' => array(
		(int) 0 => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333'
		),
		(int) 1 => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702'
		),
		(int) 2 => array(
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'tax_id' => '763042'
		),
		(int) 3 => array(
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'tax_id' => '44056'
		),
		(int) 4 => array(
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'tax_id' => '3075'
		),
		(int) 5 => array(
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'tax_id' => '41875'
		),
		(int) 6 => array(
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'tax_id' => '6239'
		),
		(int) 7 => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055'
		),
		(int) 8 => array(
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'tax_id' => '310507'
		),
		(int) 9 => array(
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'tax_id' => '2769'
		),
		(int) 10 => array(
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'tax_id' => '574566'
		),
		(int) 11 => array(
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'tax_id' => '45157'
		),
		(int) 12 => array(
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'tax_id' => '44689'
		),
		(int) 13 => array(
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'tax_id' => '7227'
		),
		(int) 14 => array(
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'tax_id' => '2880'
		),
		(int) 15 => array(
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'tax_id' => '280463'
		),
		(int) 16 => array(
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'tax_id' => '186039'
		),
		(int) 17 => array(
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'tax_id' => '130081'
		),
		(int) 18 => array(
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'tax_id' => '145475'
		),
		(int) 19 => array(
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'tax_id' => '9606'
		),
		(int) 20 => array(
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'tax_id' => '564608'
		),
		(int) 21 => array(
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'tax_id' => '296587'
		),
		(int) 22 => array(
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'tax_id' => '10090'
		),
		(int) 23 => array(
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'tax_id' => '72520'
		),
		(int) 24 => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'tax_id' => '4530'
		),
		(int) 25 => array(
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'tax_id' => '242159'
		),
		(int) 26 => array(
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'tax_id' => '1486918'
		),
		(int) 27 => array(
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'tax_id' => '385169'
		),
		(int) 28 => array(
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'tax_id' => '70448'
		),
		(int) 29 => array(
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'tax_id' => '5888'
		),
		(int) 30 => array(
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'tax_id' => '2850'
		),
		(int) 31 => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'tax_id' => '3218'
		),
		(int) 32 => array(
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'tax_id' => '67593'
		),
		(int) 33 => array(
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'tax_id' => '1470871'
		),
		(int) 34 => array(
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'tax_id' => '249344'
		),
		(int) 35 => array(
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'tax_id' => '4932'
		),
		(int) 36 => array(
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'tax_id' => '4896'
		),
		(int) 37 => array(
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'tax_id' => '35128'
		),
		(int) 38 => array(
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'tax_id' => '3067'
		)
	),
	'all_species' => array(
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702'
		),
		'acg' => array(
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'tax_id' => '763042'
		),
		'aan' => array(
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'tax_id' => '44056'
		),
		'apr' => array(
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'tax_id' => '3075'
		),
		'bprrcc1105' => array(
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'tax_id' => '41875'
		),
		'cel' => array(
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'tax_id' => '6239'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055'
		),
		'cnc64a' => array(
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'tax_id' => '310507'
		),
		'ccr' => array(
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'tax_id' => '2769'
		),
		'cvu' => array(
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'tax_id' => '574566'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'tax_id' => '45157'
		),
		'ddi' => array(
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'tax_id' => '44689'
		),
		'drm' => array(
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'tax_id' => '7227'
		),
		'esi' => array(
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'tax_id' => '2880'
		),
		'emh' => array(
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'tax_id' => '280463'
		),
		'fcy' => array(
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'tax_id' => '186039'
		),
		'gsu' => array(
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'tax_id' => '130081'
		),
		'hsp' => array(
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'tax_id' => '145475'
		),
		'hom' => array(
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'tax_id' => '9606'
		),
		'mpu' => array(
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'tax_id' => '564608'
		),
		'mrcc299' => array(
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'tax_id' => '296587'
		),
		'mus' => array(
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'tax_id' => '10090'
		),
		'nga' => array(
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'tax_id' => '72520'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'tax_id' => '4530'
		),
		'olu' => array(
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'tax_id' => '242159'
		),
		'ome' => array(
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'tax_id' => '1486918'
		),
		'orcc809' => array(
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'tax_id' => '385169'
		),
		'ota' => array(
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'tax_id' => '70448'
		),
		'pte' => array(
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'tax_id' => '5888'
		),
		'ptri' => array(
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'tax_id' => '2850'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'tax_id' => '3218'
		),
		'phs' => array(
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'tax_id' => '67593'
		),
		'pse3' => array(
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'tax_id' => '1470871'
		),
		'prcc4223' => array(
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'tax_id' => '249344'
		),
		'sac' => array(
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'tax_id' => '4932'
		),
		'scp' => array(
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'tax_id' => '4896'
		),
		'tps' => array(
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'tax_id' => '35128'
		),
		'vca' => array(
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'tax_id' => '3067'
		)
	),
	'gene_family_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'prefix' => 'HOM',
			'gene_type' => 'coding',
			'method' => '{}',
			'ancestry' => 'homology',
			'parent_id' => ''
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'prefix' => 'ORTH',
			'gene_type' => 'coding',
			'method' => '{}',
			'ancestry' => 'orthology',
			'parent_id' => 'HOMFAM'
		)
	),
	'gene_family_types_configuration' => array(),
	'data_identifier' => 'ENSMUSG00000023045',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'ENSG00000228781',
	'gf_placeholder' => 'HOM03P014763',
	'title_for_layout' => 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$similarity_hits_genes = array(
	'ENSMUSG00000023045' => array(
		'gene_id' => 'ENSMUSG00000023045',
		'e_value' => '0.0',
		'bit_score' => '1081',
		'alignment_length' => '526',
		'identity_percentage' => '100.00',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P025260'
		)
	),
	'ENSG00000167780' => array(
		'gene_id' => 'ENSG00000167780',
		'e_value' => '0.0',
		'bit_score' => '867',
		'alignment_length' => '528',
		'identity_percentage' => '81.63',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P025260'
		)
	),
	'ENSG00000057252' => array(
		'gene_id' => 'ENSG00000057252',
		'e_value' => '2e-171',
		'bit_score' => '503',
		'alignment_length' => '536',
		'identity_percentage' => '47.20',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P027874'
		)
	),
	'ENSMUSG00000026600' => array(
		'gene_id' => 'ENSMUSG00000026600',
		'e_value' => '2e-169',
		'bit_score' => '498',
		'alignment_length' => '528',
		'identity_percentage' => '46.97',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P027874'
		)
	),
	'FBgn0037612' => array(
		'gene_id' => 'FBgn0037612',
		'e_value' => '2e-70',
		'bit_score' => '241',
		'alignment_length' => '550',
		'identity_percentage' => '31.27',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P027874'
		)
	),
	'WBGene00007174' => array(
		'gene_id' => 'WBGene00007174',
		'e_value' => '4e-70',
		'bit_score' => '238',
		'alignment_length' => '460',
		'identity_percentage' => '30.43',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P027874'
		)
	),
	'pte391310' => array(
		'gene_id' => 'pte391310',
		'e_value' => '1e-60',
		'bit_score' => '215',
		'alignment_length' => '493',
		'identity_percentage' => '28.19',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P025260'
		)
	),
	'pte347260' => array(
		'gene_id' => 'pte347260',
		'e_value' => '1e-57',
		'bit_score' => '206',
		'alignment_length' => '492',
		'identity_percentage' => '27.64',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P025260'
		)
	),
	'gsu71270' => array(
		'gene_id' => 'gsu71270',
		'e_value' => '5e-36',
		'bit_score' => '144',
		'alignment_length' => '237',
		'identity_percentage' => '36.29',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'ccr43280' => array(
		'gene_id' => 'ccr43280',
		'e_value' => '1e-35',
		'bit_score' => '138',
		'alignment_length' => '240',
		'identity_percentage' => '36.67',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte337520' => array(
		'gene_id' => 'pte337520',
		'e_value' => '1e-34',
		'bit_score' => '139',
		'alignment_length' => '431',
		'identity_percentage' => '27.38',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'CM17G01990' => array(
		'gene_id' => 'CM17G01990',
		'e_value' => '1e-33',
		'bit_score' => '138',
		'alignment_length' => '240',
		'identity_percentage' => '32.08',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'DDB_G0282197' => array(
		'gene_id' => 'DDB_G0282197',
		'e_value' => '4e-32',
		'bit_score' => '132',
		'alignment_length' => '240',
		'identity_percentage' => '33.33',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P039960'
		)
	),
	'DDB_G0271342' => array(
		'gene_id' => 'DDB_G0271342',
		'e_value' => '2e-31',
		'bit_score' => '131',
		'alignment_length' => '255',
		'identity_percentage' => '32.94',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'AT2G19450' => array(
		'gene_id' => 'AT2G19450',
		'e_value' => '6e-31',
		'bit_score' => '129',
		'alignment_length' => '299',
		'identity_percentage' => '30.77',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'OS06G36800' => array(
		'gene_id' => 'OS06G36800',
		'e_value' => '1e-30',
		'bit_score' => '128',
		'alignment_length' => '256',
		'identity_percentage' => '33.20',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'CM05G01000' => array(
		'gene_id' => 'CM05G01000',
		'e_value' => '2e-30',
		'bit_score' => '128',
		'alignment_length' => '382',
		'identity_percentage' => '28.01',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P039960'
		)
	),
	'OS05G10810' => array(
		'gene_id' => 'OS05G10810',
		'e_value' => '2e-30',
		'bit_score' => '128',
		'alignment_length' => '407',
		'identity_percentage' => '27.52',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte388530' => array(
		'gene_id' => 'pte388530',
		'e_value' => '3e-30',
		'bit_score' => '126',
		'alignment_length' => '401',
		'identity_percentage' => '27.43',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'AA0044G00390' => array(
		'gene_id' => 'AA0044G00390',
		'e_value' => '3e-28',
		'bit_score' => '117',
		'alignment_length' => '229',
		'identity_percentage' => '33.62',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'gsu32710' => array(
		'gene_id' => 'gsu32710',
		'e_value' => '2e-27',
		'bit_score' => '118',
		'alignment_length' => '316',
		'identity_percentage' => '29.43',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P039960'
		)
	),
	'ATR_00036G00750' => array(
		'gene_id' => 'ATR_00036G00750',
		'e_value' => '3e-27',
		'bit_score' => '119',
		'alignment_length' => '235',
		'identity_percentage' => '31.91',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte324070' => array(
		'gene_id' => 'pte324070',
		'e_value' => '1e-26',
		'bit_score' => '116',
		'alignment_length' => '210',
		'identity_percentage' => '32.86',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'ENSG00000185000' => array(
		'gene_id' => 'ENSG00000185000',
		'e_value' => '7e-26',
		'bit_score' => '114',
		'alignment_length' => '241',
		'identity_percentage' => '31.54',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'TP02G02150' => array(
		'gene_id' => 'TP02G02150',
		'e_value' => '1e-25',
		'bit_score' => '112',
		'alignment_length' => '261',
		'identity_percentage' => '31.42',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'ccr126440' => array(
		'gene_id' => 'ccr126440',
		'e_value' => '2e-25',
		'bit_score' => '107',
		'alignment_length' => '153',
		'identity_percentage' => '38.56',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'ccr138420' => array(
		'gene_id' => 'ccr138420',
		'e_value' => '3e-25',
		'bit_score' => '106',
		'alignment_length' => '166',
		'identity_percentage' => '36.14',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte626290' => array(
		'gene_id' => 'pte626290',
		'e_value' => '6e-25',
		'bit_score' => '112',
		'alignment_length' => '246',
		'identity_percentage' => '32.93',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte535750' => array(
		'gene_id' => 'pte535750',
		'e_value' => '1e-24',
		'bit_score' => '111',
		'alignment_length' => '246',
		'identity_percentage' => '32.52',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'phs336410' => array(
		'gene_id' => 'phs336410',
		'e_value' => '4e-24',
		'bit_score' => '108',
		'alignment_length' => '271',
		'identity_percentage' => '29.52',
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'ES0074G00140' => array(
		'gene_id' => 'ES0074G00140',
		'e_value' => '5e-24',
		'bit_score' => '107',
		'alignment_length' => '247',
		'identity_percentage' => '32.39',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'CNC64A_044G00040' => array(
		'gene_id' => 'CNC64A_044G00040',
		'e_value' => '2e-23',
		'bit_score' => '107',
		'alignment_length' => '319',
		'identity_percentage' => '29.15',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'CV00G01950' => array(
		'gene_id' => 'CV00G01950',
		'e_value' => '4e-23',
		'bit_score' => '106',
		'alignment_length' => '239',
		'identity_percentage' => '31.38',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'gsu141150' => array(
		'gene_id' => 'gsu141150',
		'e_value' => '8e-23',
		'bit_score' => '105',
		'alignment_length' => '249',
		'identity_percentage' => '29.72',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P185492'
		)
	),
	'RCC4223.17g00460' => array(
		'gene_id' => 'RCC4223.17g00460',
		'e_value' => '1e-22',
		'bit_score' => '105',
		'alignment_length' => '247',
		'identity_percentage' => '31.98',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'YNR019W' => array(
		'gene_id' => 'YNR019W',
		'e_value' => '5e-22',
		'bit_score' => '103',
		'alignment_length' => '246',
		'identity_percentage' => '31.71',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'FBgn0004797' => array(
		'gene_id' => 'FBgn0004797',
		'e_value' => '1e-21',
		'bit_score' => '102',
		'alignment_length' => '235',
		'identity_percentage' => '28.94',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'PP00066G00890' => array(
		'gene_id' => 'PP00066G00890',
		'e_value' => '3e-21',
		'bit_score' => '100',
		'alignment_length' => '240',
		'identity_percentage' => '31.67',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'PI00G00180' => array(
		'gene_id' => 'PI00G00180',
		'e_value' => '3e-21',
		'bit_score' => '101',
		'alignment_length' => '175',
		'identity_percentage' => '33.71',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'AP00G04390' => array(
		'gene_id' => 'AP00G04390',
		'e_value' => '5e-21',
		'bit_score' => '100',
		'alignment_length' => '254',
		'identity_percentage' => '30.71',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'PP00131G00140' => array(
		'gene_id' => 'PP00131G00140',
		'e_value' => '4e-20',
		'bit_score' => '97.1',
		'alignment_length' => '134',
		'identity_percentage' => '35.82',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'SPAC13G7.05' => array(
		'gene_id' => 'SPAC13G7.05',
		'e_value' => '5e-20',
		'bit_score' => '97.4',
		'alignment_length' => '181',
		'identity_percentage' => '30.94',
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'Naga_101968g1' => array(
		'gene_id' => 'Naga_101968g1',
		'e_value' => '4e-19',
		'bit_score' => '89.0',
		'alignment_length' => '90',
		'identity_percentage' => '48.89',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'FC009G08820' => array(
		'gene_id' => 'FC009G08820',
		'e_value' => '1e-18',
		'bit_score' => '92.0',
		'alignment_length' => '262',
		'identity_percentage' => '30.53',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'WBGene00010408' => array(
		'gene_id' => 'WBGene00010408',
		'e_value' => '2e-18',
		'bit_score' => '92.0',
		'alignment_length' => '236',
		'identity_percentage' => '29.24',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'YCR048W' => array(
		'gene_id' => 'YCR048W',
		'e_value' => '2e-18',
		'bit_score' => '92.4',
		'alignment_length' => '205',
		'identity_percentage' => '32.68',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'emh630660' => array(
		'gene_id' => 'emh630660',
		'e_value' => '7e-17',
		'bit_score' => '83.2',
		'alignment_length' => '149',
		'identity_percentage' => '36.91',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'CR01G09980' => array(
		'gene_id' => 'CR01G09980',
		'e_value' => '1e-16',
		'bit_score' => '85.9',
		'alignment_length' => '164',
		'identity_percentage' => '34.15',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'SPCP1E11.05c' => array(
		'gene_id' => 'SPCP1E11.05c',
		'e_value' => '7e-16',
		'bit_score' => '84.3',
		'alignment_length' => '176',
		'identity_percentage' => '32.39',
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'AC00G95160' => array(
		'gene_id' => 'AC00G95160',
		'e_value' => '3e-15',
		'bit_score' => '82.0',
		'alignment_length' => '263',
		'identity_percentage' => '27.76',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte337540' => array(
		'gene_id' => 'pte337540',
		'e_value' => '3e-15',
		'bit_score' => '80.9',
		'alignment_length' => '262',
		'identity_percentage' => '30.53',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P046683'
		)
	),
	'pte374450' => array(
		'gene_id' => 'pte374450',
		'e_value' => '9e-15',
		'bit_score' => '79.7',
		'alignment_length' => '262',
		'identity_percentage' => '29.39',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P046683'
		)
	),
	'VC00G15360' => array(
		'gene_id' => 'VC00G15360',
		'e_value' => '5e-10',
		'bit_score' => '65.1',
		'alignment_length' => '250',
		'identity_percentage' => '25.20',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'DDB_G0276523' => array(
		'gene_id' => 'DDB_G0276523',
		'e_value' => '2e-07',
		'bit_score' => '57.4',
		'alignment_length' => '180',
		'identity_percentage' => '26.67',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P081488'
		)
	),
	'pte176290' => array(
		'gene_id' => 'pte176290',
		'e_value' => '1e-06',
		'bit_score' => '53.5',
		'alignment_length' => '147',
		'identity_percentage' => '26.53',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P161634'
		)
	)
)
$similarity_hits_species = array(
	'mus' => array(
		(int) 0 => 'ENSMUSG00000023045',
		(int) 1 => 'ENSMUSG00000026600'
	),
	'hom' => array(
		(int) 0 => 'ENSG00000167780',
		(int) 1 => 'ENSG00000057252',
		(int) 2 => 'ENSG00000185000'
	),
	'drm' => array(
		(int) 0 => 'FBgn0037612',
		(int) 1 => 'FBgn0004797'
	),
	'cel' => array(
		(int) 0 => 'WBGene00007174',
		(int) 1 => 'WBGene00010408'
	),
	'pte' => array(
		(int) 0 => 'pte391310',
		(int) 1 => 'pte347260',
		(int) 2 => 'pte337520',
		(int) 3 => 'pte388530',
		(int) 4 => 'pte324070',
		(int) 5 => 'pte626290',
		(int) 6 => 'pte535750',
		(int) 7 => 'pte337540',
		(int) 8 => 'pte374450',
		(int) 9 => 'pte176290'
	),
	'gsu' => array(
		(int) 0 => 'gsu71270',
		(int) 1 => 'gsu32710',
		(int) 2 => 'gsu141150'
	),
	'ccr' => array(
		(int) 0 => 'ccr43280',
		(int) 1 => 'ccr126440',
		(int) 2 => 'ccr138420'
	),
	'cme' => array(
		(int) 0 => 'CM17G01990',
		(int) 1 => 'CM05G01000'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0282197',
		(int) 1 => 'DDB_G0271342',
		(int) 2 => 'DDB_G0276523'
	),
	'ath' => array(
		(int) 0 => 'AT2G19450'
	),
	'osa' => array(
		(int) 0 => 'OS06G36800',
		(int) 1 => 'OS05G10810'
	),
	'aan' => array(
		(int) 0 => 'AA0044G00390'
	),
	'atr' => array(
		(int) 0 => 'ATR_00036G00750'
	),
	'tps' => array(
		(int) 0 => 'TP02G02150'
	),
	'phs' => array(
		(int) 0 => 'phs336410'
	),
	'esi' => array(
		(int) 0 => 'ES0074G00140'
	),
	'cvu' => array(
		(int) 0 => 'CV00G01950'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.17g00460'
	),
	'sac' => array(
		(int) 0 => 'YNR019W',
		(int) 1 => 'YCR048W'
	),
	'ppa' => array(
		(int) 0 => 'PP00066G00890',
		(int) 1 => 'PP00131G00140'
	),
	'pse3' => array(
		(int) 0 => 'PI00G00180'
	),
	'apr' => array(
		(int) 0 => 'AP00G04390'
	),
	'scp' => array(
		(int) 0 => 'SPAC13G7.05',
		(int) 1 => 'SPCP1E11.05c'
	),
	'nga' => array(
		(int) 0 => 'Naga_101968g1'
	),
	'fcy' => array(
		(int) 0 => 'FC009G08820'
	),
	'emh' => array(
		(int) 0 => 'emh630660'
	),
	'cre' => array(
		(int) 0 => 'CR01G09980'
	),
	'acg' => array(
		(int) 0 => 'AC00G95160'
	),
	'vca' => array(
		(int) 0 => 'VC00G15360'
	)
)
$gene_id = 'ENSMUSG00000023045'
$all_species_index = array(
	(int) 0 => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333'
	),
	(int) 1 => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702'
	),
	(int) 2 => array(
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'tax_id' => '763042'
	),
	(int) 3 => array(
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'tax_id' => '44056'
	),
	(int) 4 => array(
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'tax_id' => '3075'
	),
	(int) 5 => array(
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'tax_id' => '41875'
	),
	(int) 6 => array(
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'tax_id' => '6239'
	),
	(int) 7 => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055'
	),
	(int) 8 => array(
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'tax_id' => '310507'
	),
	(int) 9 => array(
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'tax_id' => '2769'
	),
	(int) 10 => array(
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'tax_id' => '574566'
	),
	(int) 11 => array(
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'tax_id' => '45157'
	),
	(int) 12 => array(
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'tax_id' => '44689'
	),
	(int) 13 => array(
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'tax_id' => '7227'
	),
	(int) 14 => array(
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'tax_id' => '2880'
	),
	(int) 15 => array(
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'tax_id' => '280463'
	),
	(int) 16 => array(
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'tax_id' => '186039'
	),
	(int) 17 => array(
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'tax_id' => '130081'
	),
	(int) 18 => array(
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'tax_id' => '145475'
	),
	(int) 19 => array(
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'tax_id' => '9606'
	),
	(int) 20 => array(
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'tax_id' => '564608'
	),
	(int) 21 => array(
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'tax_id' => '296587'
	),
	(int) 22 => array(
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'tax_id' => '10090'
	),
	(int) 23 => array(
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'tax_id' => '72520'
	),
	(int) 24 => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'tax_id' => '4530'
	),
	(int) 25 => array(
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'tax_id' => '242159'
	),
	(int) 26 => array(
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'tax_id' => '1486918'
	),
	(int) 27 => array(
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'tax_id' => '385169'
	),
	(int) 28 => array(
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'tax_id' => '70448'
	),
	(int) 29 => array(
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'tax_id' => '5888'
	),
	(int) 30 => array(
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'tax_id' => '2850'
	),
	(int) 31 => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'tax_id' => '3218'
	),
	(int) 32 => array(
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'tax_id' => '67593'
	),
	(int) 33 => array(
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'tax_id' => '1470871'
	),
	(int) 34 => array(
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'tax_id' => '249344'
	),
	(int) 35 => array(
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'tax_id' => '4932'
	),
	(int) 36 => array(
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'tax_id' => '4896'
	),
	(int) 37 => array(
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'tax_id' => '35128'
	),
	(int) 38 => array(
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'tax_id' => '3067'
	)
)
$all_species = array(
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702'
	),
	'acg' => array(
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'tax_id' => '763042'
	),
	'aan' => array(
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'tax_id' => '44056'
	),
	'apr' => array(
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'tax_id' => '3075'
	),
	'bprrcc1105' => array(
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'tax_id' => '41875'
	),
	'cel' => array(
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'tax_id' => '6239'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055'
	),
	'cnc64a' => array(
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'tax_id' => '310507'
	),
	'ccr' => array(
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'tax_id' => '2769'
	),
	'cvu' => array(
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'tax_id' => '574566'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'tax_id' => '45157'
	),
	'ddi' => array(
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'tax_id' => '44689'
	),
	'drm' => array(
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'tax_id' => '7227'
	),
	'esi' => array(
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'tax_id' => '2880'
	),
	'emh' => array(
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'tax_id' => '280463'
	),
	'fcy' => array(
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'tax_id' => '186039'
	),
	'gsu' => array(
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'tax_id' => '130081'
	),
	'hsp' => array(
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'tax_id' => '145475'
	),
	'hom' => array(
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'tax_id' => '9606'
	),
	'mpu' => array(
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'tax_id' => '564608'
	),
	'mrcc299' => array(
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'tax_id' => '296587'
	),
	'mus' => array(
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'tax_id' => '10090'
	),
	'nga' => array(
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'tax_id' => '72520'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'tax_id' => '4530'
	),
	'olu' => array(
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'tax_id' => '242159'
	),
	'ome' => array(
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'tax_id' => '1486918'
	),
	'orcc809' => array(
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'tax_id' => '385169'
	),
	'ota' => array(
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'tax_id' => '70448'
	),
	'pte' => array(
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'tax_id' => '5888'
	),
	'ptri' => array(
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'tax_id' => '2850'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'tax_id' => '3218'
	),
	'phs' => array(
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'tax_id' => '67593'
	),
	'pse3' => array(
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'tax_id' => '1470871'
	),
	'prcc4223' => array(
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'tax_id' => '249344'
	),
	'sac' => array(
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'tax_id' => '4932'
	),
	'scp' => array(
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'tax_id' => '4896'
	),
	'tps' => array(
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'tax_id' => '35128'
	),
	'vca' => array(
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'tax_id' => '3067'
	)
)
$gene_family_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'prefix' => 'HOM',
		'gene_type' => 'coding',
		'method' => '{}',
		'ancestry' => 'homology',
		'parent_id' => ''
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'prefix' => 'ORTH',
		'gene_type' => 'coding',
		'method' => '{}',
		'ancestry' => 'orthology',
		'parent_id' => 'HOMFAM'
	)
)
$gene_family_types_configuration = array()
$data_identifier = 'ENSMUSG00000023045'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'ENSG00000228781'
$gf_placeholder = 'HOM03P014763'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_044G00040',
	'e_value' => '2e-23',
	'bit_score' => '107',
	'alignment_length' => '319',
	'identity_percentage' => '29.15',
	'gf' => array(
		'HOMFAM' => 'HOM03P001013',
		'ORTHOFAM' => 'ORTHO03P001783'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00040'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146

Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]
Code Context
                                                    echo "<td><input type='checkbox' name='selected_genes[]' value='".$similarity_hit['gene_id']."' ".$checked." /></td>\n";
                                                    echo "<td>".$this->Html->link($similarity_hit_gene,array("controller"=>"genes","action"=>"view",$similarity_hit_gene),array("target"=>"_blank"))."</td>\n";
                                                    echo "<td>".$this->Html->link($similarity_hit['common_name'],array("controller"=>"organism","action"=>"view",urlencode($similarity_hit['common_name'])))."</td>\n";
$viewFile = '/xtras/group/biocomp/plaza/versions/plaza_pico_03/app/View/Analysis/custom_tree_creation.ctp'
$dataForView = array(
	'allowed_extra_sequences_types' => array(
		'aa' => 'Protein',
		'dna' => 'DNA'
	),
	'allowed_editing_methods' => array(
		'column' => 'Positions only',
		'row' => 'Genes only',
		'column_row' => 'Positions and Genes',
		'none' => 'No editing'
	),
	'allowed_tree_programs' => array(
		'fasttree' => 'FastTree',
		'iqtree' => 'IQ-TREE (includes model testing)',
		'raxml' => 'RAxML',
		'phyml' => 'PhyML'
	),
	'allowed_msa_programs' => array(
		'muscle' => 'MUSCLE',
		'mafft' => 'MAFFT'
	),
	'allowed_number_blasthits' => array(
		(int) 0 => 'all',
		(int) 1 => (int) 20,
		(int) 2 => (int) 10,
		(int) 3 => (int) 5,
		(int) 4 => (int) 1
	),
	'similarity_hits_genes' => array(
		'ENSMUSG00000023045' => array(
			'gene_id' => 'ENSMUSG00000023045',
			'e_value' => '0.0',
			'bit_score' => '1081',
			'alignment_length' => '526',
			'identity_percentage' => '100.00',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000167780' => array(
			'gene_id' => 'ENSG00000167780',
			'e_value' => '0.0',
			'bit_score' => '867',
			'alignment_length' => '528',
			'identity_percentage' => '81.63',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000057252' => array(
			'gene_id' => 'ENSG00000057252',
			'e_value' => '2e-171',
			'bit_score' => '503',
			'alignment_length' => '536',
			'identity_percentage' => '47.20',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000026600' => array(
			'gene_id' => 'ENSMUSG00000026600',
			'e_value' => '2e-169',
			'bit_score' => '498',
			'alignment_length' => '528',
			'identity_percentage' => '46.97',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0037612' => array(
			'gene_id' => 'FBgn0037612',
			'e_value' => '2e-70',
			'bit_score' => '241',
			'alignment_length' => '550',
			'identity_percentage' => '31.27',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00007174' => array(
			'gene_id' => 'WBGene00007174',
			'e_value' => '4e-70',
			'bit_score' => '238',
			'alignment_length' => '460',
			'identity_percentage' => '30.43',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte391310' => array(
			'gene_id' => 'pte391310',
			'e_value' => '1e-60',
			'bit_score' => '215',
			'alignment_length' => '493',
			'identity_percentage' => '28.19',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte347260' => array(
			'gene_id' => 'pte347260',
			'e_value' => '1e-57',
			'bit_score' => '206',
			'alignment_length' => '492',
			'identity_percentage' => '27.64',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu71270' => array(
			'gene_id' => 'gsu71270',
			'e_value' => '5e-36',
			'bit_score' => '144',
			'alignment_length' => '237',
			'identity_percentage' => '36.29',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr43280' => array(
			'gene_id' => 'ccr43280',
			'e_value' => '1e-35',
			'bit_score' => '138',
			'alignment_length' => '240',
			'identity_percentage' => '36.67',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte337520' => array(
			'gene_id' => 'pte337520',
			'e_value' => '1e-34',
			'bit_score' => '139',
			'alignment_length' => '431',
			'identity_percentage' => '27.38',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM17G01990' => array(
			'gene_id' => 'CM17G01990',
			'e_value' => '1e-33',
			'bit_score' => '138',
			'alignment_length' => '240',
			'identity_percentage' => '32.08',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0282197' => array(
			'gene_id' => 'DDB_G0282197',
			'e_value' => '4e-32',
			'bit_score' => '132',
			'alignment_length' => '240',
			'identity_percentage' => '33.33',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0271342' => array(
			'gene_id' => 'DDB_G0271342',
			'e_value' => '2e-31',
			'bit_score' => '131',
			'alignment_length' => '255',
			'identity_percentage' => '32.94',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT2G19450' => array(
			'gene_id' => 'AT2G19450',
			'e_value' => '6e-31',
			'bit_score' => '129',
			'alignment_length' => '299',
			'identity_percentage' => '30.77',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS06G36800' => array(
			'gene_id' => 'OS06G36800',
			'e_value' => '1e-30',
			'bit_score' => '128',
			'alignment_length' => '256',
			'identity_percentage' => '33.20',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM05G01000' => array(
			'gene_id' => 'CM05G01000',
			'e_value' => '2e-30',
			'bit_score' => '128',
			'alignment_length' => '382',
			'identity_percentage' => '28.01',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS05G10810' => array(
			'gene_id' => 'OS05G10810',
			'e_value' => '2e-30',
			'bit_score' => '128',
			'alignment_length' => '407',
			'identity_percentage' => '27.52',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte388530' => array(
			'gene_id' => 'pte388530',
			'e_value' => '3e-30',
			'bit_score' => '126',
			'alignment_length' => '401',
			'identity_percentage' => '27.43',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0044G00390' => array(
			'gene_id' => 'AA0044G00390',
			'e_value' => '3e-28',
			'bit_score' => '117',
			'alignment_length' => '229',
			'identity_percentage' => '33.62',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu32710' => array(
			'gene_id' => 'gsu32710',
			'e_value' => '2e-27',
			'bit_score' => '118',
			'alignment_length' => '316',
			'identity_percentage' => '29.43',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00036G00750' => array(
			'gene_id' => 'ATR_00036G00750',
			'e_value' => '3e-27',
			'bit_score' => '119',
			'alignment_length' => '235',
			'identity_percentage' => '31.91',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte324070' => array(
			'gene_id' => 'pte324070',
			'e_value' => '1e-26',
			'bit_score' => '116',
			'alignment_length' => '210',
			'identity_percentage' => '32.86',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000185000' => array(
			'gene_id' => 'ENSG00000185000',
			'e_value' => '7e-26',
			'bit_score' => '114',
			'alignment_length' => '241',
			'identity_percentage' => '31.54',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP02G02150' => array(
			'gene_id' => 'TP02G02150',
			'e_value' => '1e-25',
			'bit_score' => '112',
			'alignment_length' => '261',
			'identity_percentage' => '31.42',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr126440' => array(
			'gene_id' => 'ccr126440',
			'e_value' => '2e-25',
			'bit_score' => '107',
			'alignment_length' => '153',
			'identity_percentage' => '38.56',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr138420' => array(
			'gene_id' => 'ccr138420',
			'e_value' => '3e-25',
			'bit_score' => '106',
			'alignment_length' => '166',
			'identity_percentage' => '36.14',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte626290' => array(
			'gene_id' => 'pte626290',
			'e_value' => '6e-25',
			'bit_score' => '112',
			'alignment_length' => '246',
			'identity_percentage' => '32.93',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte535750' => array(
			'gene_id' => 'pte535750',
			'e_value' => '1e-24',
			'bit_score' => '111',
			'alignment_length' => '246',
			'identity_percentage' => '32.52',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'phs336410' => array(
			'gene_id' => 'phs336410',
			'e_value' => '4e-24',
			'bit_score' => '108',
			'alignment_length' => '271',
			'identity_percentage' => '29.52',
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0074G00140' => array(
			'gene_id' => 'ES0074G00140',
			'e_value' => '5e-24',
			'bit_score' => '107',
			'alignment_length' => '247',
			'identity_percentage' => '32.39',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_044G00040' => array(
			'gene_id' => 'CNC64A_044G00040',
			'e_value' => '2e-23',
			'bit_score' => '107',
			'alignment_length' => '319',
			'identity_percentage' => '29.15',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G01950' => array(
			'gene_id' => 'CV00G01950',
			'e_value' => '4e-23',
			'bit_score' => '106',
			'alignment_length' => '239',
			'identity_percentage' => '31.38',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu141150' => array(
			'gene_id' => 'gsu141150',
			'e_value' => '8e-23',
			'bit_score' => '105',
			'alignment_length' => '249',
			'identity_percentage' => '29.72',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.17g00460' => array(
			'gene_id' => 'RCC4223.17g00460',
			'e_value' => '1e-22',
			'bit_score' => '105',
			'alignment_length' => '247',
			'identity_percentage' => '31.98',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YNR019W' => array(
			'gene_id' => 'YNR019W',
			'e_value' => '5e-22',
			'bit_score' => '103',
			'alignment_length' => '246',
			'identity_percentage' => '31.71',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0004797' => array(
			'gene_id' => 'FBgn0004797',
			'e_value' => '1e-21',
			'bit_score' => '102',
			'alignment_length' => '235',
			'identity_percentage' => '28.94',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00066G00890' => array(
			'gene_id' => 'PP00066G00890',
			'e_value' => '3e-21',
			'bit_score' => '100',
			'alignment_length' => '240',
			'identity_percentage' => '31.67',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G00180' => array(
			'gene_id' => 'PI00G00180',
			'e_value' => '3e-21',
			'bit_score' => '101',
			'alignment_length' => '175',
			'identity_percentage' => '33.71',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G04390' => array(
			'gene_id' => 'AP00G04390',
			'e_value' => '5e-21',
			'bit_score' => '100',
			'alignment_length' => '254',
			'identity_percentage' => '30.71',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00131G00140' => array(
			'gene_id' => 'PP00131G00140',
			'e_value' => '4e-20',
			'bit_score' => '97.1',
			'alignment_length' => '134',
			'identity_percentage' => '35.82',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'SPAC13G7.05' => array(
			'gene_id' => 'SPAC13G7.05',
			'e_value' => '5e-20',
			'bit_score' => '97.4',
			'alignment_length' => '181',
			'identity_percentage' => '30.94',
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_101968g1' => array(
			'gene_id' => 'Naga_101968g1',
			'e_value' => '4e-19',
			'bit_score' => '89.0',
			'alignment_length' => '90',
			'identity_percentage' => '48.89',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC009G08820' => array(
			'gene_id' => 'FC009G08820',
			'e_value' => '1e-18',
			'bit_score' => '92.0',
			'alignment_length' => '262',
			'identity_percentage' => '30.53',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00010408' => array(
			'gene_id' => 'WBGene00010408',
			'e_value' => '2e-18',
			'bit_score' => '92.0',
			'alignment_length' => '236',
			'identity_percentage' => '29.24',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YCR048W' => array(
			'gene_id' => 'YCR048W',
			'e_value' => '2e-18',
			'bit_score' => '92.4',
			'alignment_length' => '205',
			'identity_percentage' => '32.68',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh630660' => array(
			'gene_id' => 'emh630660',
			'e_value' => '7e-17',
			'bit_score' => '83.2',
			'alignment_length' => '149',
			'identity_percentage' => '36.91',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR01G09980' => array(
			'gene_id' => 'CR01G09980',
			'e_value' => '1e-16',
			'bit_score' => '85.9',
			'alignment_length' => '164',
			'identity_percentage' => '34.15',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'SPCP1E11.05c' => array(
			'gene_id' => 'SPCP1E11.05c',
			'e_value' => '7e-16',
			'bit_score' => '84.3',
			'alignment_length' => '176',
			'identity_percentage' => '32.39',
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G95160' => array(
			'gene_id' => 'AC00G95160',
			'e_value' => '3e-15',
			'bit_score' => '82.0',
			'alignment_length' => '263',
			'identity_percentage' => '27.76',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte337540' => array(
			'gene_id' => 'pte337540',
			'e_value' => '3e-15',
			'bit_score' => '80.9',
			'alignment_length' => '262',
			'identity_percentage' => '30.53',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte374450' => array(
			'gene_id' => 'pte374450',
			'e_value' => '9e-15',
			'bit_score' => '79.7',
			'alignment_length' => '262',
			'identity_percentage' => '29.39',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G15360' => array(
			'gene_id' => 'VC00G15360',
			'e_value' => '5e-10',
			'bit_score' => '65.1',
			'alignment_length' => '250',
			'identity_percentage' => '25.20',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0276523' => array(
			'gene_id' => 'DDB_G0276523',
			'e_value' => '2e-07',
			'bit_score' => '57.4',
			'alignment_length' => '180',
			'identity_percentage' => '26.67',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte176290' => array(
			'gene_id' => 'pte176290',
			'e_value' => '1e-06',
			'bit_score' => '53.5',
			'alignment_length' => '147',
			'identity_percentage' => '26.53',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'mus' => array(
			(int) 0 => 'ENSMUSG00000023045',
			(int) 1 => 'ENSMUSG00000026600'
		),
		'hom' => array(
			(int) 0 => 'ENSG00000167780',
			(int) 1 => 'ENSG00000057252',
			(int) 2 => 'ENSG00000185000'
		),
		'drm' => array(
			(int) 0 => 'FBgn0037612',
			(int) 1 => 'FBgn0004797'
		),
		'cel' => array(
			(int) 0 => 'WBGene00007174',
			(int) 1 => 'WBGene00010408'
		),
		'pte' => array(
			(int) 0 => 'pte391310',
			(int) 1 => 'pte347260',
			(int) 2 => 'pte337520',
			(int) 3 => 'pte388530',
			(int) 4 => 'pte324070',
			(int) 5 => 'pte626290',
			(int) 6 => 'pte535750',
			(int) 7 => 'pte337540',
			(int) 8 => 'pte374450',
			(int) 9 => 'pte176290'
		),
		'gsu' => array(
			(int) 0 => 'gsu71270',
			(int) 1 => 'gsu32710',
			(int) 2 => 'gsu141150'
		),
		'ccr' => array(
			(int) 0 => 'ccr43280',
			(int) 1 => 'ccr126440',
			(int) 2 => 'ccr138420'
		),
		'cme' => array(
			(int) 0 => 'CM17G01990',
			(int) 1 => 'CM05G01000'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0282197',
			(int) 1 => 'DDB_G0271342',
			(int) 2 => 'DDB_G0276523'
		),
		'ath' => array(
			(int) 0 => 'AT2G19450'
		),
		'osa' => array(
			(int) 0 => 'OS06G36800',
			(int) 1 => 'OS05G10810'
		),
		'aan' => array(
			(int) 0 => 'AA0044G00390'
		),
		'atr' => array(
			(int) 0 => 'ATR_00036G00750'
		),
		'tps' => array(
			(int) 0 => 'TP02G02150'
		),
		'phs' => array(
			(int) 0 => 'phs336410'
		),
		'esi' => array(
			(int) 0 => 'ES0074G00140'
		),
		'cvu' => array(
			(int) 0 => 'CV00G01950'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.17g00460'
		),
		'sac' => array(
			(int) 0 => 'YNR019W',
			(int) 1 => 'YCR048W'
		),
		'ppa' => array(
			(int) 0 => 'PP00066G00890',
			(int) 1 => 'PP00131G00140'
		),
		'pse3' => array(
			(int) 0 => 'PI00G00180'
		),
		'apr' => array(
			(int) 0 => 'AP00G04390'
		),
		'scp' => array(
			(int) 0 => 'SPAC13G7.05',
			(int) 1 => 'SPCP1E11.05c'
		),
		'nga' => array(
			(int) 0 => 'Naga_101968g1'
		),
		'fcy' => array(
			(int) 0 => 'FC009G08820'
		),
		'emh' => array(
			(int) 0 => 'emh630660'
		),
		'cre' => array(
			(int) 0 => 'CR01G09980'
		),
		'acg' => array(
			(int) 0 => 'AC00G95160'
		),
		'vca' => array(
			(int) 0 => 'VC00G15360'
		)
	),
	'gene_id' => 'ENSMUSG00000023045',
	'all_species_index' => array(
		(int) 0 => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333'
		),
		(int) 1 => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702'
		),
		(int) 2 => array(
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'tax_id' => '763042'
		),
		(int) 3 => array(
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'tax_id' => '44056'
		),
		(int) 4 => array(
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'tax_id' => '3075'
		),
		(int) 5 => array(
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'tax_id' => '41875'
		),
		(int) 6 => array(
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'tax_id' => '6239'
		),
		(int) 7 => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055'
		),
		(int) 8 => array(
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'tax_id' => '310507'
		),
		(int) 9 => array(
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'tax_id' => '2769'
		),
		(int) 10 => array(
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'tax_id' => '574566'
		),
		(int) 11 => array(
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'tax_id' => '45157'
		),
		(int) 12 => array(
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'tax_id' => '44689'
		),
		(int) 13 => array(
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'tax_id' => '7227'
		),
		(int) 14 => array(
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'tax_id' => '2880'
		),
		(int) 15 => array(
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'tax_id' => '280463'
		),
		(int) 16 => array(
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'tax_id' => '186039'
		),
		(int) 17 => array(
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'tax_id' => '130081'
		),
		(int) 18 => array(
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'tax_id' => '145475'
		),
		(int) 19 => array(
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'tax_id' => '9606'
		),
		(int) 20 => array(
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'tax_id' => '564608'
		),
		(int) 21 => array(
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'tax_id' => '296587'
		),
		(int) 22 => array(
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'tax_id' => '10090'
		),
		(int) 23 => array(
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'tax_id' => '72520'
		),
		(int) 24 => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'tax_id' => '4530'
		),
		(int) 25 => array(
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'tax_id' => '242159'
		),
		(int) 26 => array(
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'tax_id' => '1486918'
		),
		(int) 27 => array(
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'tax_id' => '385169'
		),
		(int) 28 => array(
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'tax_id' => '70448'
		),
		(int) 29 => array(
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'tax_id' => '5888'
		),
		(int) 30 => array(
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'tax_id' => '2850'
		),
		(int) 31 => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'tax_id' => '3218'
		),
		(int) 32 => array(
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'tax_id' => '67593'
		),
		(int) 33 => array(
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'tax_id' => '1470871'
		),
		(int) 34 => array(
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'tax_id' => '249344'
		),
		(int) 35 => array(
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'tax_id' => '4932'
		),
		(int) 36 => array(
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'tax_id' => '4896'
		),
		(int) 37 => array(
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'tax_id' => '35128'
		),
		(int) 38 => array(
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'tax_id' => '3067'
		)
	),
	'all_species' => array(
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702'
		),
		'acg' => array(
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'tax_id' => '763042'
		),
		'aan' => array(
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'tax_id' => '44056'
		),
		'apr' => array(
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'tax_id' => '3075'
		),
		'bprrcc1105' => array(
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'tax_id' => '41875'
		),
		'cel' => array(
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'tax_id' => '6239'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055'
		),
		'cnc64a' => array(
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'tax_id' => '310507'
		),
		'ccr' => array(
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'tax_id' => '2769'
		),
		'cvu' => array(
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'tax_id' => '574566'
		),
		'cme' => array(
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'tax_id' => '45157'
		),
		'ddi' => array(
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'tax_id' => '44689'
		),
		'drm' => array(
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'tax_id' => '7227'
		),
		'esi' => array(
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'tax_id' => '2880'
		),
		'emh' => array(
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'tax_id' => '280463'
		),
		'fcy' => array(
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'tax_id' => '186039'
		),
		'gsu' => array(
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'tax_id' => '130081'
		),
		'hsp' => array(
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'tax_id' => '145475'
		),
		'hom' => array(
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'tax_id' => '9606'
		),
		'mpu' => array(
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'tax_id' => '564608'
		),
		'mrcc299' => array(
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'tax_id' => '296587'
		),
		'mus' => array(
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'tax_id' => '10090'
		),
		'nga' => array(
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'tax_id' => '72520'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'tax_id' => '4530'
		),
		'olu' => array(
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'tax_id' => '242159'
		),
		'ome' => array(
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'tax_id' => '1486918'
		),
		'orcc809' => array(
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'tax_id' => '385169'
		),
		'ota' => array(
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'tax_id' => '70448'
		),
		'pte' => array(
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'tax_id' => '5888'
		),
		'ptri' => array(
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'tax_id' => '2850'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'tax_id' => '3218'
		),
		'phs' => array(
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'tax_id' => '67593'
		),
		'pse3' => array(
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'tax_id' => '1470871'
		),
		'prcc4223' => array(
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'tax_id' => '249344'
		),
		'sac' => array(
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'tax_id' => '4932'
		),
		'scp' => array(
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'tax_id' => '4896'
		),
		'tps' => array(
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'tax_id' => '35128'
		),
		'vca' => array(
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'tax_id' => '3067'
		)
	),
	'gene_family_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'prefix' => 'HOM',
			'gene_type' => 'coding',
			'method' => '{}',
			'ancestry' => 'homology',
			'parent_id' => ''
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'prefix' => 'ORTH',
			'gene_type' => 'coding',
			'method' => '{}',
			'ancestry' => 'orthology',
			'parent_id' => 'HOMFAM'
		)
	),
	'gene_family_types_configuration' => array(),
	'data_identifier' => 'ENSMUSG00000023045',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'ENSG00000228781',
	'gf_placeholder' => 'HOM03P014763',
	'title_for_layout' => 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
)
$allowed_extra_sequences_types = array(
	'aa' => 'Protein',
	'dna' => 'DNA'
)
$allowed_editing_methods = array(
	'column' => 'Positions only',
	'row' => 'Genes only',
	'column_row' => 'Positions and Genes',
	'none' => 'No editing'
)
$allowed_tree_programs = array(
	'fasttree' => 'FastTree',
	'iqtree' => 'IQ-TREE (includes model testing)',
	'raxml' => 'RAxML',
	'phyml' => 'PhyML'
)
$allowed_msa_programs = array(
	'muscle' => 'MUSCLE',
	'mafft' => 'MAFFT'
)
$allowed_number_blasthits = array(
	(int) 0 => 'all',
	(int) 1 => (int) 20,
	(int) 2 => (int) 10,
	(int) 3 => (int) 5,
	(int) 4 => (int) 1
)
$similarity_hits_genes = array(
	'ENSMUSG00000023045' => array(
		'gene_id' => 'ENSMUSG00000023045',
		'e_value' => '0.0',
		'bit_score' => '1081',
		'alignment_length' => '526',
		'identity_percentage' => '100.00',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P025260'
		)
	),
	'ENSG00000167780' => array(
		'gene_id' => 'ENSG00000167780',
		'e_value' => '0.0',
		'bit_score' => '867',
		'alignment_length' => '528',
		'identity_percentage' => '81.63',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P025260'
		)
	),
	'ENSG00000057252' => array(
		'gene_id' => 'ENSG00000057252',
		'e_value' => '2e-171',
		'bit_score' => '503',
		'alignment_length' => '536',
		'identity_percentage' => '47.20',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P027874'
		)
	),
	'ENSMUSG00000026600' => array(
		'gene_id' => 'ENSMUSG00000026600',
		'e_value' => '2e-169',
		'bit_score' => '498',
		'alignment_length' => '528',
		'identity_percentage' => '46.97',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P027874'
		)
	),
	'FBgn0037612' => array(
		'gene_id' => 'FBgn0037612',
		'e_value' => '2e-70',
		'bit_score' => '241',
		'alignment_length' => '550',
		'identity_percentage' => '31.27',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P027874'
		)
	),
	'WBGene00007174' => array(
		'gene_id' => 'WBGene00007174',
		'e_value' => '4e-70',
		'bit_score' => '238',
		'alignment_length' => '460',
		'identity_percentage' => '30.43',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P027874'
		)
	),
	'pte391310' => array(
		'gene_id' => 'pte391310',
		'e_value' => '1e-60',
		'bit_score' => '215',
		'alignment_length' => '493',
		'identity_percentage' => '28.19',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P025260'
		)
	),
	'pte347260' => array(
		'gene_id' => 'pte347260',
		'e_value' => '1e-57',
		'bit_score' => '206',
		'alignment_length' => '492',
		'identity_percentage' => '27.64',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P025260'
		)
	),
	'gsu71270' => array(
		'gene_id' => 'gsu71270',
		'e_value' => '5e-36',
		'bit_score' => '144',
		'alignment_length' => '237',
		'identity_percentage' => '36.29',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'ccr43280' => array(
		'gene_id' => 'ccr43280',
		'e_value' => '1e-35',
		'bit_score' => '138',
		'alignment_length' => '240',
		'identity_percentage' => '36.67',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte337520' => array(
		'gene_id' => 'pte337520',
		'e_value' => '1e-34',
		'bit_score' => '139',
		'alignment_length' => '431',
		'identity_percentage' => '27.38',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'CM17G01990' => array(
		'gene_id' => 'CM17G01990',
		'e_value' => '1e-33',
		'bit_score' => '138',
		'alignment_length' => '240',
		'identity_percentage' => '32.08',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'DDB_G0282197' => array(
		'gene_id' => 'DDB_G0282197',
		'e_value' => '4e-32',
		'bit_score' => '132',
		'alignment_length' => '240',
		'identity_percentage' => '33.33',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P039960'
		)
	),
	'DDB_G0271342' => array(
		'gene_id' => 'DDB_G0271342',
		'e_value' => '2e-31',
		'bit_score' => '131',
		'alignment_length' => '255',
		'identity_percentage' => '32.94',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'AT2G19450' => array(
		'gene_id' => 'AT2G19450',
		'e_value' => '6e-31',
		'bit_score' => '129',
		'alignment_length' => '299',
		'identity_percentage' => '30.77',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'OS06G36800' => array(
		'gene_id' => 'OS06G36800',
		'e_value' => '1e-30',
		'bit_score' => '128',
		'alignment_length' => '256',
		'identity_percentage' => '33.20',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'CM05G01000' => array(
		'gene_id' => 'CM05G01000',
		'e_value' => '2e-30',
		'bit_score' => '128',
		'alignment_length' => '382',
		'identity_percentage' => '28.01',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P039960'
		)
	),
	'OS05G10810' => array(
		'gene_id' => 'OS05G10810',
		'e_value' => '2e-30',
		'bit_score' => '128',
		'alignment_length' => '407',
		'identity_percentage' => '27.52',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte388530' => array(
		'gene_id' => 'pte388530',
		'e_value' => '3e-30',
		'bit_score' => '126',
		'alignment_length' => '401',
		'identity_percentage' => '27.43',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'AA0044G00390' => array(
		'gene_id' => 'AA0044G00390',
		'e_value' => '3e-28',
		'bit_score' => '117',
		'alignment_length' => '229',
		'identity_percentage' => '33.62',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'gsu32710' => array(
		'gene_id' => 'gsu32710',
		'e_value' => '2e-27',
		'bit_score' => '118',
		'alignment_length' => '316',
		'identity_percentage' => '29.43',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P039960'
		)
	),
	'ATR_00036G00750' => array(
		'gene_id' => 'ATR_00036G00750',
		'e_value' => '3e-27',
		'bit_score' => '119',
		'alignment_length' => '235',
		'identity_percentage' => '31.91',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte324070' => array(
		'gene_id' => 'pte324070',
		'e_value' => '1e-26',
		'bit_score' => '116',
		'alignment_length' => '210',
		'identity_percentage' => '32.86',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'ENSG00000185000' => array(
		'gene_id' => 'ENSG00000185000',
		'e_value' => '7e-26',
		'bit_score' => '114',
		'alignment_length' => '241',
		'identity_percentage' => '31.54',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'TP02G02150' => array(
		'gene_id' => 'TP02G02150',
		'e_value' => '1e-25',
		'bit_score' => '112',
		'alignment_length' => '261',
		'identity_percentage' => '31.42',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'ccr126440' => array(
		'gene_id' => 'ccr126440',
		'e_value' => '2e-25',
		'bit_score' => '107',
		'alignment_length' => '153',
		'identity_percentage' => '38.56',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'ccr138420' => array(
		'gene_id' => 'ccr138420',
		'e_value' => '3e-25',
		'bit_score' => '106',
		'alignment_length' => '166',
		'identity_percentage' => '36.14',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte626290' => array(
		'gene_id' => 'pte626290',
		'e_value' => '6e-25',
		'bit_score' => '112',
		'alignment_length' => '246',
		'identity_percentage' => '32.93',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte535750' => array(
		'gene_id' => 'pte535750',
		'e_value' => '1e-24',
		'bit_score' => '111',
		'alignment_length' => '246',
		'identity_percentage' => '32.52',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'phs336410' => array(
		'gene_id' => 'phs336410',
		'e_value' => '4e-24',
		'bit_score' => '108',
		'alignment_length' => '271',
		'identity_percentage' => '29.52',
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'ES0074G00140' => array(
		'gene_id' => 'ES0074G00140',
		'e_value' => '5e-24',
		'bit_score' => '107',
		'alignment_length' => '247',
		'identity_percentage' => '32.39',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'CNC64A_044G00040' => array(
		'gene_id' => 'CNC64A_044G00040',
		'e_value' => '2e-23',
		'bit_score' => '107',
		'alignment_length' => '319',
		'identity_percentage' => '29.15',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'CV00G01950' => array(
		'gene_id' => 'CV00G01950',
		'e_value' => '4e-23',
		'bit_score' => '106',
		'alignment_length' => '239',
		'identity_percentage' => '31.38',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'gsu141150' => array(
		'gene_id' => 'gsu141150',
		'e_value' => '8e-23',
		'bit_score' => '105',
		'alignment_length' => '249',
		'identity_percentage' => '29.72',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P185492'
		)
	),
	'RCC4223.17g00460' => array(
		'gene_id' => 'RCC4223.17g00460',
		'e_value' => '1e-22',
		'bit_score' => '105',
		'alignment_length' => '247',
		'identity_percentage' => '31.98',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'YNR019W' => array(
		'gene_id' => 'YNR019W',
		'e_value' => '5e-22',
		'bit_score' => '103',
		'alignment_length' => '246',
		'identity_percentage' => '31.71',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'FBgn0004797' => array(
		'gene_id' => 'FBgn0004797',
		'e_value' => '1e-21',
		'bit_score' => '102',
		'alignment_length' => '235',
		'identity_percentage' => '28.94',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'PP00066G00890' => array(
		'gene_id' => 'PP00066G00890',
		'e_value' => '3e-21',
		'bit_score' => '100',
		'alignment_length' => '240',
		'identity_percentage' => '31.67',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'PI00G00180' => array(
		'gene_id' => 'PI00G00180',
		'e_value' => '3e-21',
		'bit_score' => '101',
		'alignment_length' => '175',
		'identity_percentage' => '33.71',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'AP00G04390' => array(
		'gene_id' => 'AP00G04390',
		'e_value' => '5e-21',
		'bit_score' => '100',
		'alignment_length' => '254',
		'identity_percentage' => '30.71',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'PP00131G00140' => array(
		'gene_id' => 'PP00131G00140',
		'e_value' => '4e-20',
		'bit_score' => '97.1',
		'alignment_length' => '134',
		'identity_percentage' => '35.82',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'SPAC13G7.05' => array(
		'gene_id' => 'SPAC13G7.05',
		'e_value' => '5e-20',
		'bit_score' => '97.4',
		'alignment_length' => '181',
		'identity_percentage' => '30.94',
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'Naga_101968g1' => array(
		'gene_id' => 'Naga_101968g1',
		'e_value' => '4e-19',
		'bit_score' => '89.0',
		'alignment_length' => '90',
		'identity_percentage' => '48.89',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'FC009G08820' => array(
		'gene_id' => 'FC009G08820',
		'e_value' => '1e-18',
		'bit_score' => '92.0',
		'alignment_length' => '262',
		'identity_percentage' => '30.53',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'WBGene00010408' => array(
		'gene_id' => 'WBGene00010408',
		'e_value' => '2e-18',
		'bit_score' => '92.0',
		'alignment_length' => '236',
		'identity_percentage' => '29.24',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'YCR048W' => array(
		'gene_id' => 'YCR048W',
		'e_value' => '2e-18',
		'bit_score' => '92.4',
		'alignment_length' => '205',
		'identity_percentage' => '32.68',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P012270'
		)
	),
	'emh630660' => array(
		'gene_id' => 'emh630660',
		'e_value' => '7e-17',
		'bit_score' => '83.2',
		'alignment_length' => '149',
		'identity_percentage' => '36.91',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'CR01G09980' => array(
		'gene_id' => 'CR01G09980',
		'e_value' => '1e-16',
		'bit_score' => '85.9',
		'alignment_length' => '164',
		'identity_percentage' => '34.15',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'SPCP1E11.05c' => array(
		'gene_id' => 'SPCP1E11.05c',
		'e_value' => '7e-16',
		'bit_score' => '84.3',
		'alignment_length' => '176',
		'identity_percentage' => '32.39',
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'AC00G95160' => array(
		'gene_id' => 'AC00G95160',
		'e_value' => '3e-15',
		'bit_score' => '82.0',
		'alignment_length' => '263',
		'identity_percentage' => '27.76',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'pte337540' => array(
		'gene_id' => 'pte337540',
		'e_value' => '3e-15',
		'bit_score' => '80.9',
		'alignment_length' => '262',
		'identity_percentage' => '30.53',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P046683'
		)
	),
	'pte374450' => array(
		'gene_id' => 'pte374450',
		'e_value' => '9e-15',
		'bit_score' => '79.7',
		'alignment_length' => '262',
		'identity_percentage' => '29.39',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P046683'
		)
	),
	'VC00G15360' => array(
		'gene_id' => 'VC00G15360',
		'e_value' => '5e-10',
		'bit_score' => '65.1',
		'alignment_length' => '250',
		'identity_percentage' => '25.20',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P001783'
		)
	),
	'DDB_G0276523' => array(
		'gene_id' => 'DDB_G0276523',
		'e_value' => '2e-07',
		'bit_score' => '57.4',
		'alignment_length' => '180',
		'identity_percentage' => '26.67',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P081488'
		)
	),
	'pte176290' => array(
		'gene_id' => 'pte176290',
		'e_value' => '1e-06',
		'bit_score' => '53.5',
		'alignment_length' => '147',
		'identity_percentage' => '26.53',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001013',
			'ORTHOFAM' => 'ORTHO03P161634'
		)
	)
)
$similarity_hits_species = array(
	'mus' => array(
		(int) 0 => 'ENSMUSG00000023045',
		(int) 1 => 'ENSMUSG00000026600'
	),
	'hom' => array(
		(int) 0 => 'ENSG00000167780',
		(int) 1 => 'ENSG00000057252',
		(int) 2 => 'ENSG00000185000'
	),
	'drm' => array(
		(int) 0 => 'FBgn0037612',
		(int) 1 => 'FBgn0004797'
	),
	'cel' => array(
		(int) 0 => 'WBGene00007174',
		(int) 1 => 'WBGene00010408'
	),
	'pte' => array(
		(int) 0 => 'pte391310',
		(int) 1 => 'pte347260',
		(int) 2 => 'pte337520',
		(int) 3 => 'pte388530',
		(int) 4 => 'pte324070',
		(int) 5 => 'pte626290',
		(int) 6 => 'pte535750',
		(int) 7 => 'pte337540',
		(int) 8 => 'pte374450',
		(int) 9 => 'pte176290'
	),
	'gsu' => array(
		(int) 0 => 'gsu71270',
		(int) 1 => 'gsu32710',
		(int) 2 => 'gsu141150'
	),
	'ccr' => array(
		(int) 0 => 'ccr43280',
		(int) 1 => 'ccr126440',
		(int) 2 => 'ccr138420'
	),
	'cme' => array(
		(int) 0 => 'CM17G01990',
		(int) 1 => 'CM05G01000'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0282197',
		(int) 1 => 'DDB_G0271342',
		(int) 2 => 'DDB_G0276523'
	),
	'ath' => array(
		(int) 0 => 'AT2G19450'
	),
	'osa' => array(
		(int) 0 => 'OS06G36800',
		(int) 1 => 'OS05G10810'
	),
	'aan' => array(
		(int) 0 => 'AA0044G00390'
	),
	'atr' => array(
		(int) 0 => 'ATR_00036G00750'
	),
	'tps' => array(
		(int) 0 => 'TP02G02150'
	),
	'phs' => array(
		(int) 0 => 'phs336410'
	),
	'esi' => array(
		(int) 0 => 'ES0074G00140'
	),
	'cvu' => array(
		(int) 0 => 'CV00G01950'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.17g00460'
	),
	'sac' => array(
		(int) 0 => 'YNR019W',
		(int) 1 => 'YCR048W'
	),
	'ppa' => array(
		(int) 0 => 'PP00066G00890',
		(int) 1 => 'PP00131G00140'
	),
	'pse3' => array(
		(int) 0 => 'PI00G00180'
	),
	'apr' => array(
		(int) 0 => 'AP00G04390'
	),
	'scp' => array(
		(int) 0 => 'SPAC13G7.05',
		(int) 1 => 'SPCP1E11.05c'
	),
	'nga' => array(
		(int) 0 => 'Naga_101968g1'
	),
	'fcy' => array(
		(int) 0 => 'FC009G08820'
	),
	'emh' => array(
		(int) 0 => 'emh630660'
	),
	'cre' => array(
		(int) 0 => 'CR01G09980'
	),
	'acg' => array(
		(int) 0 => 'AC00G95160'
	),
	'vca' => array(
		(int) 0 => 'VC00G15360'
	)
)
$gene_id = 'ENSMUSG00000023045'
$all_species_index = array(
	(int) 0 => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333'
	),
	(int) 1 => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702'
	),
	(int) 2 => array(
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'tax_id' => '763042'
	),
	(int) 3 => array(
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'tax_id' => '44056'
	),
	(int) 4 => array(
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'tax_id' => '3075'
	),
	(int) 5 => array(
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'tax_id' => '41875'
	),
	(int) 6 => array(
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'tax_id' => '6239'
	),
	(int) 7 => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055'
	),
	(int) 8 => array(
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'tax_id' => '310507'
	),
	(int) 9 => array(
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'tax_id' => '2769'
	),
	(int) 10 => array(
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'tax_id' => '574566'
	),
	(int) 11 => array(
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'tax_id' => '45157'
	),
	(int) 12 => array(
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'tax_id' => '44689'
	),
	(int) 13 => array(
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'tax_id' => '7227'
	),
	(int) 14 => array(
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'tax_id' => '2880'
	),
	(int) 15 => array(
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'tax_id' => '280463'
	),
	(int) 16 => array(
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'tax_id' => '186039'
	),
	(int) 17 => array(
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'tax_id' => '130081'
	),
	(int) 18 => array(
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'tax_id' => '145475'
	),
	(int) 19 => array(
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'tax_id' => '9606'
	),
	(int) 20 => array(
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'tax_id' => '564608'
	),
	(int) 21 => array(
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'tax_id' => '296587'
	),
	(int) 22 => array(
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'tax_id' => '10090'
	),
	(int) 23 => array(
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'tax_id' => '72520'
	),
	(int) 24 => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'tax_id' => '4530'
	),
	(int) 25 => array(
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'tax_id' => '242159'
	),
	(int) 26 => array(
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'tax_id' => '1486918'
	),
	(int) 27 => array(
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'tax_id' => '385169'
	),
	(int) 28 => array(
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'tax_id' => '70448'
	),
	(int) 29 => array(
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'tax_id' => '5888'
	),
	(int) 30 => array(
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'tax_id' => '2850'
	),
	(int) 31 => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'tax_id' => '3218'
	),
	(int) 32 => array(
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'tax_id' => '67593'
	),
	(int) 33 => array(
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'tax_id' => '1470871'
	),
	(int) 34 => array(
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'tax_id' => '249344'
	),
	(int) 35 => array(
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'tax_id' => '4932'
	),
	(int) 36 => array(
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'tax_id' => '4896'
	),
	(int) 37 => array(
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'tax_id' => '35128'
	),
	(int) 38 => array(
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'tax_id' => '3067'
	)
)
$all_species = array(
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702'
	),
	'acg' => array(
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'tax_id' => '763042'
	),
	'aan' => array(
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'tax_id' => '44056'
	),
	'apr' => array(
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'tax_id' => '3075'
	),
	'bprrcc1105' => array(
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'tax_id' => '41875'
	),
	'cel' => array(
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'tax_id' => '6239'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055'
	),
	'cnc64a' => array(
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'tax_id' => '310507'
	),
	'ccr' => array(
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'tax_id' => '2769'
	),
	'cvu' => array(
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'tax_id' => '574566'
	),
	'cme' => array(
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'tax_id' => '45157'
	),
	'ddi' => array(
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'tax_id' => '44689'
	),
	'drm' => array(
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'tax_id' => '7227'
	),
	'esi' => array(
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'tax_id' => '2880'
	),
	'emh' => array(
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'tax_id' => '280463'
	),
	'fcy' => array(
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'tax_id' => '186039'
	),
	'gsu' => array(
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'tax_id' => '130081'
	),
	'hsp' => array(
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'tax_id' => '145475'
	),
	'hom' => array(
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'tax_id' => '9606'
	),
	'mpu' => array(
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'tax_id' => '564608'
	),
	'mrcc299' => array(
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'tax_id' => '296587'
	),
	'mus' => array(
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'tax_id' => '10090'
	),
	'nga' => array(
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'tax_id' => '72520'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'tax_id' => '4530'
	),
	'olu' => array(
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'tax_id' => '242159'
	),
	'ome' => array(
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'tax_id' => '1486918'
	),
	'orcc809' => array(
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'tax_id' => '385169'
	),
	'ota' => array(
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'tax_id' => '70448'
	),
	'pte' => array(
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'tax_id' => '5888'
	),
	'ptri' => array(
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'tax_id' => '2850'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'tax_id' => '3218'
	),
	'phs' => array(
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'tax_id' => '67593'
	),
	'pse3' => array(
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'tax_id' => '1470871'
	),
	'prcc4223' => array(
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'tax_id' => '249344'
	),
	'sac' => array(
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'tax_id' => '4932'
	),
	'scp' => array(
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'tax_id' => '4896'
	),
	'tps' => array(
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'tax_id' => '35128'
	),
	'vca' => array(
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'tax_id' => '3067'
	)
)
$gene_family_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'prefix' => 'HOM',
		'gene_type' => 'coding',
		'method' => '{}',
		'ancestry' => 'homology',
		'parent_id' => ''
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'prefix' => 'ORTH',
		'gene_type' => 'coding',
		'method' => '{}',
		'ancestry' => 'orthology',
		'parent_id' => 'HOMFAM'
	)
)
$gene_family_types_configuration = array()
$data_identifier = 'ENSMUSG00000023045'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'ENSG00000228781'
$gf_placeholder = 'HOM03P014763'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_044G00040',
	'e_value' => '2e-23',
	'bit_score' => '107',
	'alignment_length' => '319',
	'identity_percentage' => '29.15',
	'gf' => array(
		'HOMFAM' => 'HOM03P001013',
		'ORTHOFAM' => 'ORTHO03P001783'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00040'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146