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(
		'ORCC809_02G02560' => array(
			'gene_id' => 'ORCC809_02G02560',
			'e_value' => '5e-54',
			'bit_score' => '168',
			'alignment_length' => '79',
			'identity_percentage' => '100.00',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G45231' => array(
			'gene_id' => 'AT1G45231',
			'e_value' => '4e-21',
			'bit_score' => '90.5',
			'alignment_length' => '79',
			'identity_percentage' => '51.90',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OM_04G01940' => array(
			'gene_id' => 'OM_04G01940',
			'e_value' => '9e-21',
			'bit_score' => '87.4',
			'alignment_length' => '84',
			'identity_percentage' => '48.81',
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0288547' => array(
			'gene_id' => 'DDB_G0288547',
			'e_value' => '2e-19',
			'bit_score' => '84.0',
			'alignment_length' => '80',
			'identity_percentage' => '50.00',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00003G02210' => array(
			'gene_id' => 'ATR_00003G02210',
			'e_value' => '4e-19',
			'bit_score' => '85.5',
			'alignment_length' => '79',
			'identity_percentage' => '50.63',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL02G04740' => array(
			'gene_id' => 'OL02G04740',
			'e_value' => '8e-19',
			'bit_score' => '79.0',
			'alignment_length' => '82',
			'identity_percentage' => '50.00',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr132780' => array(
			'gene_id' => 'ccr132780',
			'e_value' => '1e-18',
			'bit_score' => '80.9',
			'alignment_length' => '79',
			'identity_percentage' => '55.70',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000028233' => array(
			'gene_id' => 'ENSMUSG00000028233',
			'e_value' => '3e-18',
			'bit_score' => '83.2',
			'alignment_length' => '79',
			'identity_percentage' => '50.63',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000093862' => array(
			'gene_id' => 'ENSMUSG00000093862',
			'e_value' => '4e-18',
			'bit_score' => '82.8',
			'alignment_length' => '79',
			'identity_percentage' => '50.63',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0120G00110' => array(
			'gene_id' => 'ES0120G00110',
			'e_value' => '8e-18',
			'bit_score' => '81.3',
			'alignment_length' => '80',
			'identity_percentage' => '51.25',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G95840' => array(
			'gene_id' => 'AC00G95840',
			'e_value' => '1e-17',
			'bit_score' => '78.2',
			'alignment_length' => '80',
			'identity_percentage' => '50.00',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00092G00090' => array(
			'gene_id' => 'PP00092G00090',
			'e_value' => '1e-17',
			'bit_score' => '80.9',
			'alignment_length' => '79',
			'identity_percentage' => '49.37',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh729020' => array(
			'gene_id' => 'emh729020',
			'e_value' => '2e-17',
			'bit_score' => '79.0',
			'alignment_length' => '79',
			'identity_percentage' => '51.90',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100003g58' => array(
			'gene_id' => 'Naga_100003g58',
			'e_value' => '3e-17',
			'bit_score' => '79.3',
			'alignment_length' => '79',
			'identity_percentage' => '49.37',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_044G00080' => array(
			'gene_id' => 'CNC64A_044G00080',
			'e_value' => '4e-17',
			'bit_score' => '78.2',
			'alignment_length' => '79',
			'identity_percentage' => '49.37',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OT_02G01350' => array(
			'gene_id' => 'OT_02G01350',
			'e_value' => '7e-17',
			'bit_score' => '75.9',
			'alignment_length' => '82',
			'identity_percentage' => '46.34',
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MRCC299_01G06910' => array(
			'gene_id' => 'MRCC299_01G06910',
			'e_value' => '8e-17',
			'bit_score' => '78.2',
			'alignment_length' => '96',
			'identity_percentage' => '44.79',
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G27930' => array(
			'gene_id' => 'OS03G27930',
			'e_value' => '2e-16',
			'bit_score' => '77.4',
			'alignment_length' => '79',
			'identity_percentage' => '46.84',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.19g00730' => array(
			'gene_id' => 'RCC4223.19g00730',
			'e_value' => '6e-16',
			'bit_score' => '75.9',
			'alignment_length' => '79',
			'identity_percentage' => '49.37',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_22G00250' => array(
			'gene_id' => 'PTI_22G00250',
			'e_value' => '8e-16',
			'bit_score' => '75.5',
			'alignment_length' => '80',
			'identity_percentage' => '50.00',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G01490' => array(
			'gene_id' => 'PI00G01490',
			'e_value' => '1e-15',
			'bit_score' => '75.1',
			'alignment_length' => '79',
			'identity_percentage' => '50.63',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0266195' => array(
			'gene_id' => 'FBgn0266195',
			'e_value' => '3e-15',
			'bit_score' => '73.9',
			'alignment_length' => '80',
			'identity_percentage' => '45.00',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G30550' => array(
			'gene_id' => 'AT1G30550',
			'e_value' => '3e-15',
			'bit_score' => '73.6',
			'alignment_length' => '79',
			'identity_percentage' => '48.10',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00019G00550' => array(
			'gene_id' => 'ATR_00019G00550',
			'e_value' => '1e-14',
			'bit_score' => '70.9',
			'alignment_length' => '79',
			'identity_percentage' => '45.57',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G61210' => array(
			'gene_id' => 'CV00G61210',
			'e_value' => '2e-14',
			'bit_score' => '68.9',
			'alignment_length' => '78',
			'identity_percentage' => '43.59',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0018G01160' => array(
			'gene_id' => 'AA0018G01160',
			'e_value' => '2e-14',
			'bit_score' => '67.8',
			'alignment_length' => '79',
			'identity_percentage' => '44.30',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_22G00920' => array(
			'gene_id' => 'PTI_22G00920',
			'e_value' => '2e-14',
			'bit_score' => '70.5',
			'alignment_length' => '70',
			'identity_percentage' => '51.43',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP02G08210' => array(
			'gene_id' => 'TP02G08210',
			'e_value' => '4e-14',
			'bit_score' => '68.9',
			'alignment_length' => '76',
			'identity_percentage' => '44.74',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00011631' => array(
			'gene_id' => 'WBGene00011631',
			'e_value' => '5e-14',
			'bit_score' => '70.5',
			'alignment_length' => '79',
			'identity_percentage' => '46.84',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR06G11280' => array(
			'gene_id' => 'CR06G11280',
			'e_value' => '2e-13',
			'bit_score' => '69.3',
			'alignment_length' => '75',
			'identity_percentage' => '48.00',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP07G02910' => array(
			'gene_id' => 'TP07G02910',
			'e_value' => '4e-13',
			'bit_score' => '64.7',
			'alignment_length' => '73',
			'identity_percentage' => '43.84',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'BPRRCC1105_14G03340' => array(
			'gene_id' => 'BPRRCC1105_14G03340',
			'e_value' => '5e-13',
			'bit_score' => '65.1',
			'alignment_length' => '80',
			'identity_percentage' => '41.25',
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC009G01340' => array(
			'gene_id' => 'FC009G01340',
			'e_value' => '1e-11',
			'bit_score' => '61.6',
			'alignment_length' => '71',
			'identity_percentage' => '45.07',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu74830' => array(
			'gene_id' => 'gsu74830',
			'e_value' => '3e-11',
			'bit_score' => '60.8',
			'alignment_length' => '80',
			'identity_percentage' => '42.50',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'phs121750' => array(
			'gene_id' => 'phs121750',
			'e_value' => '3e-11',
			'bit_score' => '62.0',
			'alignment_length' => '80',
			'identity_percentage' => '42.50',
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte317770' => array(
			'gene_id' => 'pte317770',
			'e_value' => '1e-10',
			'bit_score' => '59.3',
			'alignment_length' => '82',
			'identity_percentage' => '39.02',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G00630' => array(
			'gene_id' => 'AP00G00630',
			'e_value' => '1e-10',
			'bit_score' => '60.8',
			'alignment_length' => '63',
			'identity_percentage' => '47.62',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'SPAC2G11.15c' => array(
			'gene_id' => 'SPAC2G11.15c',
			'e_value' => '2e-10',
			'bit_score' => '58.5',
			'alignment_length' => '68',
			'identity_percentage' => '42.65',
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte492450' => array(
			'gene_id' => 'pte492450',
			'e_value' => '2e-10',
			'bit_score' => '58.9',
			'alignment_length' => '79',
			'identity_percentage' => '41.77',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC004G05310' => array(
			'gene_id' => 'FC004G05310',
			'e_value' => '5e-09',
			'bit_score' => '54.7',
			'alignment_length' => '72',
			'identity_percentage' => '44.44',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YPL157W' => array(
			'gene_id' => 'YPL157W',
			'e_value' => '1e-08',
			'bit_score' => '54.3',
			'alignment_length' => '71',
			'identity_percentage' => '42.25',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MP02G06160' => array(
			'gene_id' => 'MP02G06160',
			'e_value' => '1e-07',
			'bit_score' => '51.6',
			'alignment_length' => '103',
			'identity_percentage' => '38.83',
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS06G08800' => array(
			'gene_id' => 'OS06G08800',
			'e_value' => '2e-07',
			'bit_score' => '51.2',
			'alignment_length' => '66',
			'identity_percentage' => '46.97',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte644480' => array(
			'gene_id' => 'pte644480',
			'e_value' => '6e-07',
			'bit_score' => '48.9',
			'alignment_length' => '61',
			'identity_percentage' => '40.98',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'orcc809' => array(
			(int) 0 => 'ORCC809_02G02560'
		),
		'ath' => array(
			(int) 0 => 'AT1G45231',
			(int) 1 => 'AT1G30550'
		),
		'ome' => array(
			(int) 0 => 'OM_04G01940'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0288547'
		),
		'atr' => array(
			(int) 0 => 'ATR_00003G02210',
			(int) 1 => 'ATR_00019G00550'
		),
		'olu' => array(
			(int) 0 => 'OL02G04740'
		),
		'ccr' => array(
			(int) 0 => 'ccr132780'
		),
		'mus' => array(
			(int) 0 => 'ENSMUSG00000028233',
			(int) 1 => 'ENSMUSG00000093862'
		),
		'esi' => array(
			(int) 0 => 'ES0120G00110'
		),
		'acg' => array(
			(int) 0 => 'AC00G95840'
		),
		'ppa' => array(
			(int) 0 => 'PP00092G00090'
		),
		'emh' => array(
			(int) 0 => 'emh729020'
		),
		'nga' => array(
			(int) 0 => 'Naga_100003g58'
		),
		'ota' => array(
			(int) 0 => 'OT_02G01350'
		),
		'mrcc299' => array(
			(int) 0 => 'MRCC299_01G06910'
		),
		'osa' => array(
			(int) 0 => 'OS03G27930',
			(int) 1 => 'OS06G08800'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.19g00730'
		),
		'ptri' => array(
			(int) 0 => 'PTI_22G00250',
			(int) 1 => 'PTI_22G00920'
		),
		'pse3' => array(
			(int) 0 => 'PI00G01490'
		),
		'drm' => array(
			(int) 0 => 'FBgn0266195'
		),
		'cvu' => array(
			(int) 0 => 'CV00G61210'
		),
		'aan' => array(
			(int) 0 => 'AA0018G01160'
		),
		'tps' => array(
			(int) 0 => 'TP02G08210',
			(int) 1 => 'TP07G02910'
		),
		'cel' => array(
			(int) 0 => 'WBGene00011631'
		),
		'cre' => array(
			(int) 0 => 'CR06G11280'
		),
		'bprrcc1105' => array(
			(int) 0 => 'BPRRCC1105_14G03340'
		),
		'fcy' => array(
			(int) 0 => 'FC009G01340',
			(int) 1 => 'FC004G05310'
		),
		'gsu' => array(
			(int) 0 => 'gsu74830'
		),
		'phs' => array(
			(int) 0 => 'phs121750'
		),
		'pte' => array(
			(int) 0 => 'pte317770',
			(int) 1 => 'pte492450',
			(int) 2 => 'pte644480'
		),
		'apr' => array(
			(int) 0 => 'AP00G00630'
		),
		'scp' => array(
			(int) 0 => 'SPAC2G11.15c'
		),
		'sac' => array(
			(int) 0 => 'YPL157W'
		),
		'mpu' => array(
			(int) 0 => 'MP02G06160'
		)
	),
	'gene_id' => 'ORCC809_02G02560',
	'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' => 'ORCC809_02G02560',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'OT_04G04440',
	'gf_placeholder' => 'HOM03P024521',
	'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(
	'ORCC809_02G02560' => array(
		'gene_id' => 'ORCC809_02G02560',
		'e_value' => '5e-54',
		'bit_score' => '168',
		'alignment_length' => '79',
		'identity_percentage' => '100.00',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AT1G45231' => array(
		'gene_id' => 'AT1G45231',
		'e_value' => '4e-21',
		'bit_score' => '90.5',
		'alignment_length' => '79',
		'identity_percentage' => '51.90',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OM_04G01940' => array(
		'gene_id' => 'OM_04G01940',
		'e_value' => '9e-21',
		'bit_score' => '87.4',
		'alignment_length' => '84',
		'identity_percentage' => '48.81',
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'DDB_G0288547' => array(
		'gene_id' => 'DDB_G0288547',
		'e_value' => '2e-19',
		'bit_score' => '84.0',
		'alignment_length' => '80',
		'identity_percentage' => '50.00',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ATR_00003G02210' => array(
		'gene_id' => 'ATR_00003G02210',
		'e_value' => '4e-19',
		'bit_score' => '85.5',
		'alignment_length' => '79',
		'identity_percentage' => '50.63',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OL02G04740' => array(
		'gene_id' => 'OL02G04740',
		'e_value' => '8e-19',
		'bit_score' => '79.0',
		'alignment_length' => '82',
		'identity_percentage' => '50.00',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ccr132780' => array(
		'gene_id' => 'ccr132780',
		'e_value' => '1e-18',
		'bit_score' => '80.9',
		'alignment_length' => '79',
		'identity_percentage' => '55.70',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ENSMUSG00000028233' => array(
		'gene_id' => 'ENSMUSG00000028233',
		'e_value' => '3e-18',
		'bit_score' => '83.2',
		'alignment_length' => '79',
		'identity_percentage' => '50.63',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ENSMUSG00000093862' => array(
		'gene_id' => 'ENSMUSG00000093862',
		'e_value' => '4e-18',
		'bit_score' => '82.8',
		'alignment_length' => '79',
		'identity_percentage' => '50.63',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ES0120G00110' => array(
		'gene_id' => 'ES0120G00110',
		'e_value' => '8e-18',
		'bit_score' => '81.3',
		'alignment_length' => '80',
		'identity_percentage' => '51.25',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AC00G95840' => array(
		'gene_id' => 'AC00G95840',
		'e_value' => '1e-17',
		'bit_score' => '78.2',
		'alignment_length' => '80',
		'identity_percentage' => '50.00',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'PP00092G00090' => array(
		'gene_id' => 'PP00092G00090',
		'e_value' => '1e-17',
		'bit_score' => '80.9',
		'alignment_length' => '79',
		'identity_percentage' => '49.37',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'emh729020' => array(
		'gene_id' => 'emh729020',
		'e_value' => '2e-17',
		'bit_score' => '79.0',
		'alignment_length' => '79',
		'identity_percentage' => '51.90',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'Naga_100003g58' => array(
		'gene_id' => 'Naga_100003g58',
		'e_value' => '3e-17',
		'bit_score' => '79.3',
		'alignment_length' => '79',
		'identity_percentage' => '49.37',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'CNC64A_044G00080' => array(
		'gene_id' => 'CNC64A_044G00080',
		'e_value' => '4e-17',
		'bit_score' => '78.2',
		'alignment_length' => '79',
		'identity_percentage' => '49.37',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OT_02G01350' => array(
		'gene_id' => 'OT_02G01350',
		'e_value' => '7e-17',
		'bit_score' => '75.9',
		'alignment_length' => '82',
		'identity_percentage' => '46.34',
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'MRCC299_01G06910' => array(
		'gene_id' => 'MRCC299_01G06910',
		'e_value' => '8e-17',
		'bit_score' => '78.2',
		'alignment_length' => '96',
		'identity_percentage' => '44.79',
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OS03G27930' => array(
		'gene_id' => 'OS03G27930',
		'e_value' => '2e-16',
		'bit_score' => '77.4',
		'alignment_length' => '79',
		'identity_percentage' => '46.84',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'RCC4223.19g00730' => array(
		'gene_id' => 'RCC4223.19g00730',
		'e_value' => '6e-16',
		'bit_score' => '75.9',
		'alignment_length' => '79',
		'identity_percentage' => '49.37',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'PTI_22G00250' => array(
		'gene_id' => 'PTI_22G00250',
		'e_value' => '8e-16',
		'bit_score' => '75.5',
		'alignment_length' => '80',
		'identity_percentage' => '50.00',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P064266'
		)
	),
	'PI00G01490' => array(
		'gene_id' => 'PI00G01490',
		'e_value' => '1e-15',
		'bit_score' => '75.1',
		'alignment_length' => '79',
		'identity_percentage' => '50.63',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'FBgn0266195' => array(
		'gene_id' => 'FBgn0266195',
		'e_value' => '3e-15',
		'bit_score' => '73.9',
		'alignment_length' => '80',
		'identity_percentage' => '45.00',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AT1G30550' => array(
		'gene_id' => 'AT1G30550',
		'e_value' => '3e-15',
		'bit_score' => '73.6',
		'alignment_length' => '79',
		'identity_percentage' => '48.10',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ATR_00019G00550' => array(
		'gene_id' => 'ATR_00019G00550',
		'e_value' => '1e-14',
		'bit_score' => '70.9',
		'alignment_length' => '79',
		'identity_percentage' => '45.57',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'CV00G61210' => array(
		'gene_id' => 'CV00G61210',
		'e_value' => '2e-14',
		'bit_score' => '68.9',
		'alignment_length' => '78',
		'identity_percentage' => '43.59',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AA0018G01160' => array(
		'gene_id' => 'AA0018G01160',
		'e_value' => '2e-14',
		'bit_score' => '67.8',
		'alignment_length' => '79',
		'identity_percentage' => '44.30',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'PTI_22G00920' => array(
		'gene_id' => 'PTI_22G00920',
		'e_value' => '2e-14',
		'bit_score' => '70.5',
		'alignment_length' => '70',
		'identity_percentage' => '51.43',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'TP02G08210' => array(
		'gene_id' => 'TP02G08210',
		'e_value' => '4e-14',
		'bit_score' => '68.9',
		'alignment_length' => '76',
		'identity_percentage' => '44.74',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'WBGene00011631' => array(
		'gene_id' => 'WBGene00011631',
		'e_value' => '5e-14',
		'bit_score' => '70.5',
		'alignment_length' => '79',
		'identity_percentage' => '46.84',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'CR06G11280' => array(
		'gene_id' => 'CR06G11280',
		'e_value' => '2e-13',
		'bit_score' => '69.3',
		'alignment_length' => '75',
		'identity_percentage' => '48.00',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'TP07G02910' => array(
		'gene_id' => 'TP07G02910',
		'e_value' => '4e-13',
		'bit_score' => '64.7',
		'alignment_length' => '73',
		'identity_percentage' => '43.84',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P079127'
		)
	),
	'BPRRCC1105_14G03340' => array(
		'gene_id' => 'BPRRCC1105_14G03340',
		'e_value' => '5e-13',
		'bit_score' => '65.1',
		'alignment_length' => '80',
		'identity_percentage' => '41.25',
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'FC009G01340' => array(
		'gene_id' => 'FC009G01340',
		'e_value' => '1e-11',
		'bit_score' => '61.6',
		'alignment_length' => '71',
		'identity_percentage' => '45.07',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'gsu74830' => array(
		'gene_id' => 'gsu74830',
		'e_value' => '3e-11',
		'bit_score' => '60.8',
		'alignment_length' => '80',
		'identity_percentage' => '42.50',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'phs121750' => array(
		'gene_id' => 'phs121750',
		'e_value' => '3e-11',
		'bit_score' => '62.0',
		'alignment_length' => '80',
		'identity_percentage' => '42.50',
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'pte317770' => array(
		'gene_id' => 'pte317770',
		'e_value' => '1e-10',
		'bit_score' => '59.3',
		'alignment_length' => '82',
		'identity_percentage' => '39.02',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AP00G00630' => array(
		'gene_id' => 'AP00G00630',
		'e_value' => '1e-10',
		'bit_score' => '60.8',
		'alignment_length' => '63',
		'identity_percentage' => '47.62',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'SPAC2G11.15c' => array(
		'gene_id' => 'SPAC2G11.15c',
		'e_value' => '2e-10',
		'bit_score' => '58.5',
		'alignment_length' => '68',
		'identity_percentage' => '42.65',
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'pte492450' => array(
		'gene_id' => 'pte492450',
		'e_value' => '2e-10',
		'bit_score' => '58.9',
		'alignment_length' => '79',
		'identity_percentage' => '41.77',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'FC004G05310' => array(
		'gene_id' => 'FC004G05310',
		'e_value' => '5e-09',
		'bit_score' => '54.7',
		'alignment_length' => '72',
		'identity_percentage' => '44.44',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P064266'
		)
	),
	'YPL157W' => array(
		'gene_id' => 'YPL157W',
		'e_value' => '1e-08',
		'bit_score' => '54.3',
		'alignment_length' => '71',
		'identity_percentage' => '42.25',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'MP02G06160' => array(
		'gene_id' => 'MP02G06160',
		'e_value' => '1e-07',
		'bit_score' => '51.6',
		'alignment_length' => '103',
		'identity_percentage' => '38.83',
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OS06G08800' => array(
		'gene_id' => 'OS06G08800',
		'e_value' => '2e-07',
		'bit_score' => '51.2',
		'alignment_length' => '66',
		'identity_percentage' => '46.97',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'pte644480' => array(
		'gene_id' => 'pte644480',
		'e_value' => '6e-07',
		'bit_score' => '48.9',
		'alignment_length' => '61',
		'identity_percentage' => '40.98',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	)
)
$similarity_hits_species = array(
	'orcc809' => array(
		(int) 0 => 'ORCC809_02G02560'
	),
	'ath' => array(
		(int) 0 => 'AT1G45231',
		(int) 1 => 'AT1G30550'
	),
	'ome' => array(
		(int) 0 => 'OM_04G01940'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0288547'
	),
	'atr' => array(
		(int) 0 => 'ATR_00003G02210',
		(int) 1 => 'ATR_00019G00550'
	),
	'olu' => array(
		(int) 0 => 'OL02G04740'
	),
	'ccr' => array(
		(int) 0 => 'ccr132780'
	),
	'mus' => array(
		(int) 0 => 'ENSMUSG00000028233',
		(int) 1 => 'ENSMUSG00000093862'
	),
	'esi' => array(
		(int) 0 => 'ES0120G00110'
	),
	'acg' => array(
		(int) 0 => 'AC00G95840'
	),
	'ppa' => array(
		(int) 0 => 'PP00092G00090'
	),
	'emh' => array(
		(int) 0 => 'emh729020'
	),
	'nga' => array(
		(int) 0 => 'Naga_100003g58'
	),
	'ota' => array(
		(int) 0 => 'OT_02G01350'
	),
	'mrcc299' => array(
		(int) 0 => 'MRCC299_01G06910'
	),
	'osa' => array(
		(int) 0 => 'OS03G27930',
		(int) 1 => 'OS06G08800'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.19g00730'
	),
	'ptri' => array(
		(int) 0 => 'PTI_22G00250',
		(int) 1 => 'PTI_22G00920'
	),
	'pse3' => array(
		(int) 0 => 'PI00G01490'
	),
	'drm' => array(
		(int) 0 => 'FBgn0266195'
	),
	'cvu' => array(
		(int) 0 => 'CV00G61210'
	),
	'aan' => array(
		(int) 0 => 'AA0018G01160'
	),
	'tps' => array(
		(int) 0 => 'TP02G08210',
		(int) 1 => 'TP07G02910'
	),
	'cel' => array(
		(int) 0 => 'WBGene00011631'
	),
	'cre' => array(
		(int) 0 => 'CR06G11280'
	),
	'bprrcc1105' => array(
		(int) 0 => 'BPRRCC1105_14G03340'
	),
	'fcy' => array(
		(int) 0 => 'FC009G01340',
		(int) 1 => 'FC004G05310'
	),
	'gsu' => array(
		(int) 0 => 'gsu74830'
	),
	'phs' => array(
		(int) 0 => 'phs121750'
	),
	'pte' => array(
		(int) 0 => 'pte317770',
		(int) 1 => 'pte492450',
		(int) 2 => 'pte644480'
	),
	'apr' => array(
		(int) 0 => 'AP00G00630'
	),
	'scp' => array(
		(int) 0 => 'SPAC2G11.15c'
	),
	'sac' => array(
		(int) 0 => 'YPL157W'
	),
	'mpu' => array(
		(int) 0 => 'MP02G06160'
	)
)
$gene_id = 'ORCC809_02G02560'
$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 = 'ORCC809_02G02560'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'OT_04G04440'
$gf_placeholder = 'HOM03P024521'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_044G00080',
	'e_value' => '4e-17',
	'bit_score' => '78.2',
	'alignment_length' => '79',
	'identity_percentage' => '49.37',
	'gf' => array(
		'HOMFAM' => 'HOM03P001586',
		'ORTHOFAM' => 'ORTHO03P000813'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00080'
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(
		'ORCC809_02G02560' => array(
			'gene_id' => 'ORCC809_02G02560',
			'e_value' => '5e-54',
			'bit_score' => '168',
			'alignment_length' => '79',
			'identity_percentage' => '100.00',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G45231' => array(
			'gene_id' => 'AT1G45231',
			'e_value' => '4e-21',
			'bit_score' => '90.5',
			'alignment_length' => '79',
			'identity_percentage' => '51.90',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OM_04G01940' => array(
			'gene_id' => 'OM_04G01940',
			'e_value' => '9e-21',
			'bit_score' => '87.4',
			'alignment_length' => '84',
			'identity_percentage' => '48.81',
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0288547' => array(
			'gene_id' => 'DDB_G0288547',
			'e_value' => '2e-19',
			'bit_score' => '84.0',
			'alignment_length' => '80',
			'identity_percentage' => '50.00',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00003G02210' => array(
			'gene_id' => 'ATR_00003G02210',
			'e_value' => '4e-19',
			'bit_score' => '85.5',
			'alignment_length' => '79',
			'identity_percentage' => '50.63',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL02G04740' => array(
			'gene_id' => 'OL02G04740',
			'e_value' => '8e-19',
			'bit_score' => '79.0',
			'alignment_length' => '82',
			'identity_percentage' => '50.00',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr132780' => array(
			'gene_id' => 'ccr132780',
			'e_value' => '1e-18',
			'bit_score' => '80.9',
			'alignment_length' => '79',
			'identity_percentage' => '55.70',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000028233' => array(
			'gene_id' => 'ENSMUSG00000028233',
			'e_value' => '3e-18',
			'bit_score' => '83.2',
			'alignment_length' => '79',
			'identity_percentage' => '50.63',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000093862' => array(
			'gene_id' => 'ENSMUSG00000093862',
			'e_value' => '4e-18',
			'bit_score' => '82.8',
			'alignment_length' => '79',
			'identity_percentage' => '50.63',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0120G00110' => array(
			'gene_id' => 'ES0120G00110',
			'e_value' => '8e-18',
			'bit_score' => '81.3',
			'alignment_length' => '80',
			'identity_percentage' => '51.25',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G95840' => array(
			'gene_id' => 'AC00G95840',
			'e_value' => '1e-17',
			'bit_score' => '78.2',
			'alignment_length' => '80',
			'identity_percentage' => '50.00',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00092G00090' => array(
			'gene_id' => 'PP00092G00090',
			'e_value' => '1e-17',
			'bit_score' => '80.9',
			'alignment_length' => '79',
			'identity_percentage' => '49.37',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh729020' => array(
			'gene_id' => 'emh729020',
			'e_value' => '2e-17',
			'bit_score' => '79.0',
			'alignment_length' => '79',
			'identity_percentage' => '51.90',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100003g58' => array(
			'gene_id' => 'Naga_100003g58',
			'e_value' => '3e-17',
			'bit_score' => '79.3',
			'alignment_length' => '79',
			'identity_percentage' => '49.37',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_044G00080' => array(
			'gene_id' => 'CNC64A_044G00080',
			'e_value' => '4e-17',
			'bit_score' => '78.2',
			'alignment_length' => '79',
			'identity_percentage' => '49.37',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OT_02G01350' => array(
			'gene_id' => 'OT_02G01350',
			'e_value' => '7e-17',
			'bit_score' => '75.9',
			'alignment_length' => '82',
			'identity_percentage' => '46.34',
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MRCC299_01G06910' => array(
			'gene_id' => 'MRCC299_01G06910',
			'e_value' => '8e-17',
			'bit_score' => '78.2',
			'alignment_length' => '96',
			'identity_percentage' => '44.79',
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G27930' => array(
			'gene_id' => 'OS03G27930',
			'e_value' => '2e-16',
			'bit_score' => '77.4',
			'alignment_length' => '79',
			'identity_percentage' => '46.84',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.19g00730' => array(
			'gene_id' => 'RCC4223.19g00730',
			'e_value' => '6e-16',
			'bit_score' => '75.9',
			'alignment_length' => '79',
			'identity_percentage' => '49.37',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_22G00250' => array(
			'gene_id' => 'PTI_22G00250',
			'e_value' => '8e-16',
			'bit_score' => '75.5',
			'alignment_length' => '80',
			'identity_percentage' => '50.00',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G01490' => array(
			'gene_id' => 'PI00G01490',
			'e_value' => '1e-15',
			'bit_score' => '75.1',
			'alignment_length' => '79',
			'identity_percentage' => '50.63',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0266195' => array(
			'gene_id' => 'FBgn0266195',
			'e_value' => '3e-15',
			'bit_score' => '73.9',
			'alignment_length' => '80',
			'identity_percentage' => '45.00',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G30550' => array(
			'gene_id' => 'AT1G30550',
			'e_value' => '3e-15',
			'bit_score' => '73.6',
			'alignment_length' => '79',
			'identity_percentage' => '48.10',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00019G00550' => array(
			'gene_id' => 'ATR_00019G00550',
			'e_value' => '1e-14',
			'bit_score' => '70.9',
			'alignment_length' => '79',
			'identity_percentage' => '45.57',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G61210' => array(
			'gene_id' => 'CV00G61210',
			'e_value' => '2e-14',
			'bit_score' => '68.9',
			'alignment_length' => '78',
			'identity_percentage' => '43.59',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0018G01160' => array(
			'gene_id' => 'AA0018G01160',
			'e_value' => '2e-14',
			'bit_score' => '67.8',
			'alignment_length' => '79',
			'identity_percentage' => '44.30',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_22G00920' => array(
			'gene_id' => 'PTI_22G00920',
			'e_value' => '2e-14',
			'bit_score' => '70.5',
			'alignment_length' => '70',
			'identity_percentage' => '51.43',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP02G08210' => array(
			'gene_id' => 'TP02G08210',
			'e_value' => '4e-14',
			'bit_score' => '68.9',
			'alignment_length' => '76',
			'identity_percentage' => '44.74',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00011631' => array(
			'gene_id' => 'WBGene00011631',
			'e_value' => '5e-14',
			'bit_score' => '70.5',
			'alignment_length' => '79',
			'identity_percentage' => '46.84',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR06G11280' => array(
			'gene_id' => 'CR06G11280',
			'e_value' => '2e-13',
			'bit_score' => '69.3',
			'alignment_length' => '75',
			'identity_percentage' => '48.00',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP07G02910' => array(
			'gene_id' => 'TP07G02910',
			'e_value' => '4e-13',
			'bit_score' => '64.7',
			'alignment_length' => '73',
			'identity_percentage' => '43.84',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'BPRRCC1105_14G03340' => array(
			'gene_id' => 'BPRRCC1105_14G03340',
			'e_value' => '5e-13',
			'bit_score' => '65.1',
			'alignment_length' => '80',
			'identity_percentage' => '41.25',
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC009G01340' => array(
			'gene_id' => 'FC009G01340',
			'e_value' => '1e-11',
			'bit_score' => '61.6',
			'alignment_length' => '71',
			'identity_percentage' => '45.07',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu74830' => array(
			'gene_id' => 'gsu74830',
			'e_value' => '3e-11',
			'bit_score' => '60.8',
			'alignment_length' => '80',
			'identity_percentage' => '42.50',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'phs121750' => array(
			'gene_id' => 'phs121750',
			'e_value' => '3e-11',
			'bit_score' => '62.0',
			'alignment_length' => '80',
			'identity_percentage' => '42.50',
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte317770' => array(
			'gene_id' => 'pte317770',
			'e_value' => '1e-10',
			'bit_score' => '59.3',
			'alignment_length' => '82',
			'identity_percentage' => '39.02',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G00630' => array(
			'gene_id' => 'AP00G00630',
			'e_value' => '1e-10',
			'bit_score' => '60.8',
			'alignment_length' => '63',
			'identity_percentage' => '47.62',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'SPAC2G11.15c' => array(
			'gene_id' => 'SPAC2G11.15c',
			'e_value' => '2e-10',
			'bit_score' => '58.5',
			'alignment_length' => '68',
			'identity_percentage' => '42.65',
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte492450' => array(
			'gene_id' => 'pte492450',
			'e_value' => '2e-10',
			'bit_score' => '58.9',
			'alignment_length' => '79',
			'identity_percentage' => '41.77',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC004G05310' => array(
			'gene_id' => 'FC004G05310',
			'e_value' => '5e-09',
			'bit_score' => '54.7',
			'alignment_length' => '72',
			'identity_percentage' => '44.44',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YPL157W' => array(
			'gene_id' => 'YPL157W',
			'e_value' => '1e-08',
			'bit_score' => '54.3',
			'alignment_length' => '71',
			'identity_percentage' => '42.25',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MP02G06160' => array(
			'gene_id' => 'MP02G06160',
			'e_value' => '1e-07',
			'bit_score' => '51.6',
			'alignment_length' => '103',
			'identity_percentage' => '38.83',
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS06G08800' => array(
			'gene_id' => 'OS06G08800',
			'e_value' => '2e-07',
			'bit_score' => '51.2',
			'alignment_length' => '66',
			'identity_percentage' => '46.97',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte644480' => array(
			'gene_id' => 'pte644480',
			'e_value' => '6e-07',
			'bit_score' => '48.9',
			'alignment_length' => '61',
			'identity_percentage' => '40.98',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'orcc809' => array(
			(int) 0 => 'ORCC809_02G02560'
		),
		'ath' => array(
			(int) 0 => 'AT1G45231',
			(int) 1 => 'AT1G30550'
		),
		'ome' => array(
			(int) 0 => 'OM_04G01940'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0288547'
		),
		'atr' => array(
			(int) 0 => 'ATR_00003G02210',
			(int) 1 => 'ATR_00019G00550'
		),
		'olu' => array(
			(int) 0 => 'OL02G04740'
		),
		'ccr' => array(
			(int) 0 => 'ccr132780'
		),
		'mus' => array(
			(int) 0 => 'ENSMUSG00000028233',
			(int) 1 => 'ENSMUSG00000093862'
		),
		'esi' => array(
			(int) 0 => 'ES0120G00110'
		),
		'acg' => array(
			(int) 0 => 'AC00G95840'
		),
		'ppa' => array(
			(int) 0 => 'PP00092G00090'
		),
		'emh' => array(
			(int) 0 => 'emh729020'
		),
		'nga' => array(
			(int) 0 => 'Naga_100003g58'
		),
		'ota' => array(
			(int) 0 => 'OT_02G01350'
		),
		'mrcc299' => array(
			(int) 0 => 'MRCC299_01G06910'
		),
		'osa' => array(
			(int) 0 => 'OS03G27930',
			(int) 1 => 'OS06G08800'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.19g00730'
		),
		'ptri' => array(
			(int) 0 => 'PTI_22G00250',
			(int) 1 => 'PTI_22G00920'
		),
		'pse3' => array(
			(int) 0 => 'PI00G01490'
		),
		'drm' => array(
			(int) 0 => 'FBgn0266195'
		),
		'cvu' => array(
			(int) 0 => 'CV00G61210'
		),
		'aan' => array(
			(int) 0 => 'AA0018G01160'
		),
		'tps' => array(
			(int) 0 => 'TP02G08210',
			(int) 1 => 'TP07G02910'
		),
		'cel' => array(
			(int) 0 => 'WBGene00011631'
		),
		'cre' => array(
			(int) 0 => 'CR06G11280'
		),
		'bprrcc1105' => array(
			(int) 0 => 'BPRRCC1105_14G03340'
		),
		'fcy' => array(
			(int) 0 => 'FC009G01340',
			(int) 1 => 'FC004G05310'
		),
		'gsu' => array(
			(int) 0 => 'gsu74830'
		),
		'phs' => array(
			(int) 0 => 'phs121750'
		),
		'pte' => array(
			(int) 0 => 'pte317770',
			(int) 1 => 'pte492450',
			(int) 2 => 'pte644480'
		),
		'apr' => array(
			(int) 0 => 'AP00G00630'
		),
		'scp' => array(
			(int) 0 => 'SPAC2G11.15c'
		),
		'sac' => array(
			(int) 0 => 'YPL157W'
		),
		'mpu' => array(
			(int) 0 => 'MP02G06160'
		)
	),
	'gene_id' => 'ORCC809_02G02560',
	'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' => 'ORCC809_02G02560',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'OT_04G04440',
	'gf_placeholder' => 'HOM03P024521',
	'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(
	'ORCC809_02G02560' => array(
		'gene_id' => 'ORCC809_02G02560',
		'e_value' => '5e-54',
		'bit_score' => '168',
		'alignment_length' => '79',
		'identity_percentage' => '100.00',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AT1G45231' => array(
		'gene_id' => 'AT1G45231',
		'e_value' => '4e-21',
		'bit_score' => '90.5',
		'alignment_length' => '79',
		'identity_percentage' => '51.90',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OM_04G01940' => array(
		'gene_id' => 'OM_04G01940',
		'e_value' => '9e-21',
		'bit_score' => '87.4',
		'alignment_length' => '84',
		'identity_percentage' => '48.81',
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'DDB_G0288547' => array(
		'gene_id' => 'DDB_G0288547',
		'e_value' => '2e-19',
		'bit_score' => '84.0',
		'alignment_length' => '80',
		'identity_percentage' => '50.00',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ATR_00003G02210' => array(
		'gene_id' => 'ATR_00003G02210',
		'e_value' => '4e-19',
		'bit_score' => '85.5',
		'alignment_length' => '79',
		'identity_percentage' => '50.63',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OL02G04740' => array(
		'gene_id' => 'OL02G04740',
		'e_value' => '8e-19',
		'bit_score' => '79.0',
		'alignment_length' => '82',
		'identity_percentage' => '50.00',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ccr132780' => array(
		'gene_id' => 'ccr132780',
		'e_value' => '1e-18',
		'bit_score' => '80.9',
		'alignment_length' => '79',
		'identity_percentage' => '55.70',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ENSMUSG00000028233' => array(
		'gene_id' => 'ENSMUSG00000028233',
		'e_value' => '3e-18',
		'bit_score' => '83.2',
		'alignment_length' => '79',
		'identity_percentage' => '50.63',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ENSMUSG00000093862' => array(
		'gene_id' => 'ENSMUSG00000093862',
		'e_value' => '4e-18',
		'bit_score' => '82.8',
		'alignment_length' => '79',
		'identity_percentage' => '50.63',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ES0120G00110' => array(
		'gene_id' => 'ES0120G00110',
		'e_value' => '8e-18',
		'bit_score' => '81.3',
		'alignment_length' => '80',
		'identity_percentage' => '51.25',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AC00G95840' => array(
		'gene_id' => 'AC00G95840',
		'e_value' => '1e-17',
		'bit_score' => '78.2',
		'alignment_length' => '80',
		'identity_percentage' => '50.00',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'PP00092G00090' => array(
		'gene_id' => 'PP00092G00090',
		'e_value' => '1e-17',
		'bit_score' => '80.9',
		'alignment_length' => '79',
		'identity_percentage' => '49.37',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'emh729020' => array(
		'gene_id' => 'emh729020',
		'e_value' => '2e-17',
		'bit_score' => '79.0',
		'alignment_length' => '79',
		'identity_percentage' => '51.90',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'Naga_100003g58' => array(
		'gene_id' => 'Naga_100003g58',
		'e_value' => '3e-17',
		'bit_score' => '79.3',
		'alignment_length' => '79',
		'identity_percentage' => '49.37',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'CNC64A_044G00080' => array(
		'gene_id' => 'CNC64A_044G00080',
		'e_value' => '4e-17',
		'bit_score' => '78.2',
		'alignment_length' => '79',
		'identity_percentage' => '49.37',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OT_02G01350' => array(
		'gene_id' => 'OT_02G01350',
		'e_value' => '7e-17',
		'bit_score' => '75.9',
		'alignment_length' => '82',
		'identity_percentage' => '46.34',
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'MRCC299_01G06910' => array(
		'gene_id' => 'MRCC299_01G06910',
		'e_value' => '8e-17',
		'bit_score' => '78.2',
		'alignment_length' => '96',
		'identity_percentage' => '44.79',
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OS03G27930' => array(
		'gene_id' => 'OS03G27930',
		'e_value' => '2e-16',
		'bit_score' => '77.4',
		'alignment_length' => '79',
		'identity_percentage' => '46.84',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'RCC4223.19g00730' => array(
		'gene_id' => 'RCC4223.19g00730',
		'e_value' => '6e-16',
		'bit_score' => '75.9',
		'alignment_length' => '79',
		'identity_percentage' => '49.37',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'PTI_22G00250' => array(
		'gene_id' => 'PTI_22G00250',
		'e_value' => '8e-16',
		'bit_score' => '75.5',
		'alignment_length' => '80',
		'identity_percentage' => '50.00',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P064266'
		)
	),
	'PI00G01490' => array(
		'gene_id' => 'PI00G01490',
		'e_value' => '1e-15',
		'bit_score' => '75.1',
		'alignment_length' => '79',
		'identity_percentage' => '50.63',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'FBgn0266195' => array(
		'gene_id' => 'FBgn0266195',
		'e_value' => '3e-15',
		'bit_score' => '73.9',
		'alignment_length' => '80',
		'identity_percentage' => '45.00',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AT1G30550' => array(
		'gene_id' => 'AT1G30550',
		'e_value' => '3e-15',
		'bit_score' => '73.6',
		'alignment_length' => '79',
		'identity_percentage' => '48.10',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ATR_00019G00550' => array(
		'gene_id' => 'ATR_00019G00550',
		'e_value' => '1e-14',
		'bit_score' => '70.9',
		'alignment_length' => '79',
		'identity_percentage' => '45.57',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'CV00G61210' => array(
		'gene_id' => 'CV00G61210',
		'e_value' => '2e-14',
		'bit_score' => '68.9',
		'alignment_length' => '78',
		'identity_percentage' => '43.59',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AA0018G01160' => array(
		'gene_id' => 'AA0018G01160',
		'e_value' => '2e-14',
		'bit_score' => '67.8',
		'alignment_length' => '79',
		'identity_percentage' => '44.30',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'PTI_22G00920' => array(
		'gene_id' => 'PTI_22G00920',
		'e_value' => '2e-14',
		'bit_score' => '70.5',
		'alignment_length' => '70',
		'identity_percentage' => '51.43',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'TP02G08210' => array(
		'gene_id' => 'TP02G08210',
		'e_value' => '4e-14',
		'bit_score' => '68.9',
		'alignment_length' => '76',
		'identity_percentage' => '44.74',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'WBGene00011631' => array(
		'gene_id' => 'WBGene00011631',
		'e_value' => '5e-14',
		'bit_score' => '70.5',
		'alignment_length' => '79',
		'identity_percentage' => '46.84',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'CR06G11280' => array(
		'gene_id' => 'CR06G11280',
		'e_value' => '2e-13',
		'bit_score' => '69.3',
		'alignment_length' => '75',
		'identity_percentage' => '48.00',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'TP07G02910' => array(
		'gene_id' => 'TP07G02910',
		'e_value' => '4e-13',
		'bit_score' => '64.7',
		'alignment_length' => '73',
		'identity_percentage' => '43.84',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P079127'
		)
	),
	'BPRRCC1105_14G03340' => array(
		'gene_id' => 'BPRRCC1105_14G03340',
		'e_value' => '5e-13',
		'bit_score' => '65.1',
		'alignment_length' => '80',
		'identity_percentage' => '41.25',
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'FC009G01340' => array(
		'gene_id' => 'FC009G01340',
		'e_value' => '1e-11',
		'bit_score' => '61.6',
		'alignment_length' => '71',
		'identity_percentage' => '45.07',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'gsu74830' => array(
		'gene_id' => 'gsu74830',
		'e_value' => '3e-11',
		'bit_score' => '60.8',
		'alignment_length' => '80',
		'identity_percentage' => '42.50',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'phs121750' => array(
		'gene_id' => 'phs121750',
		'e_value' => '3e-11',
		'bit_score' => '62.0',
		'alignment_length' => '80',
		'identity_percentage' => '42.50',
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'pte317770' => array(
		'gene_id' => 'pte317770',
		'e_value' => '1e-10',
		'bit_score' => '59.3',
		'alignment_length' => '82',
		'identity_percentage' => '39.02',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'AP00G00630' => array(
		'gene_id' => 'AP00G00630',
		'e_value' => '1e-10',
		'bit_score' => '60.8',
		'alignment_length' => '63',
		'identity_percentage' => '47.62',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'SPAC2G11.15c' => array(
		'gene_id' => 'SPAC2G11.15c',
		'e_value' => '2e-10',
		'bit_score' => '58.5',
		'alignment_length' => '68',
		'identity_percentage' => '42.65',
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'pte492450' => array(
		'gene_id' => 'pte492450',
		'e_value' => '2e-10',
		'bit_score' => '58.9',
		'alignment_length' => '79',
		'identity_percentage' => '41.77',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'FC004G05310' => array(
		'gene_id' => 'FC004G05310',
		'e_value' => '5e-09',
		'bit_score' => '54.7',
		'alignment_length' => '72',
		'identity_percentage' => '44.44',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P064266'
		)
	),
	'YPL157W' => array(
		'gene_id' => 'YPL157W',
		'e_value' => '1e-08',
		'bit_score' => '54.3',
		'alignment_length' => '71',
		'identity_percentage' => '42.25',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'MP02G06160' => array(
		'gene_id' => 'MP02G06160',
		'e_value' => '1e-07',
		'bit_score' => '51.6',
		'alignment_length' => '103',
		'identity_percentage' => '38.83',
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'OS06G08800' => array(
		'gene_id' => 'OS06G08800',
		'e_value' => '2e-07',
		'bit_score' => '51.2',
		'alignment_length' => '66',
		'identity_percentage' => '46.97',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'pte644480' => array(
		'gene_id' => 'pte644480',
		'e_value' => '6e-07',
		'bit_score' => '48.9',
		'alignment_length' => '61',
		'identity_percentage' => '40.98',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	)
)
$similarity_hits_species = array(
	'orcc809' => array(
		(int) 0 => 'ORCC809_02G02560'
	),
	'ath' => array(
		(int) 0 => 'AT1G45231',
		(int) 1 => 'AT1G30550'
	),
	'ome' => array(
		(int) 0 => 'OM_04G01940'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0288547'
	),
	'atr' => array(
		(int) 0 => 'ATR_00003G02210',
		(int) 1 => 'ATR_00019G00550'
	),
	'olu' => array(
		(int) 0 => 'OL02G04740'
	),
	'ccr' => array(
		(int) 0 => 'ccr132780'
	),
	'mus' => array(
		(int) 0 => 'ENSMUSG00000028233',
		(int) 1 => 'ENSMUSG00000093862'
	),
	'esi' => array(
		(int) 0 => 'ES0120G00110'
	),
	'acg' => array(
		(int) 0 => 'AC00G95840'
	),
	'ppa' => array(
		(int) 0 => 'PP00092G00090'
	),
	'emh' => array(
		(int) 0 => 'emh729020'
	),
	'nga' => array(
		(int) 0 => 'Naga_100003g58'
	),
	'ota' => array(
		(int) 0 => 'OT_02G01350'
	),
	'mrcc299' => array(
		(int) 0 => 'MRCC299_01G06910'
	),
	'osa' => array(
		(int) 0 => 'OS03G27930',
		(int) 1 => 'OS06G08800'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.19g00730'
	),
	'ptri' => array(
		(int) 0 => 'PTI_22G00250',
		(int) 1 => 'PTI_22G00920'
	),
	'pse3' => array(
		(int) 0 => 'PI00G01490'
	),
	'drm' => array(
		(int) 0 => 'FBgn0266195'
	),
	'cvu' => array(
		(int) 0 => 'CV00G61210'
	),
	'aan' => array(
		(int) 0 => 'AA0018G01160'
	),
	'tps' => array(
		(int) 0 => 'TP02G08210',
		(int) 1 => 'TP07G02910'
	),
	'cel' => array(
		(int) 0 => 'WBGene00011631'
	),
	'cre' => array(
		(int) 0 => 'CR06G11280'
	),
	'bprrcc1105' => array(
		(int) 0 => 'BPRRCC1105_14G03340'
	),
	'fcy' => array(
		(int) 0 => 'FC009G01340',
		(int) 1 => 'FC004G05310'
	),
	'gsu' => array(
		(int) 0 => 'gsu74830'
	),
	'phs' => array(
		(int) 0 => 'phs121750'
	),
	'pte' => array(
		(int) 0 => 'pte317770',
		(int) 1 => 'pte492450',
		(int) 2 => 'pte644480'
	),
	'apr' => array(
		(int) 0 => 'AP00G00630'
	),
	'scp' => array(
		(int) 0 => 'SPAC2G11.15c'
	),
	'sac' => array(
		(int) 0 => 'YPL157W'
	),
	'mpu' => array(
		(int) 0 => 'MP02G06160'
	)
)
$gene_id = 'ORCC809_02G02560'
$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 = 'ORCC809_02G02560'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'OT_04G04440'
$gf_placeholder = 'HOM03P024521'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_044G00080',
	'e_value' => '4e-17',
	'bit_score' => '78.2',
	'alignment_length' => '79',
	'identity_percentage' => '49.37',
	'gf' => array(
		'HOMFAM' => 'HOM03P001586',
		'ORTHOFAM' => 'ORTHO03P000813'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00080'
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