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(
		'ES0121G00230' => array(
			'gene_id' => 'ES0121G00230',
			'e_value' => '0.0',
			'bit_score' => '667',
			'alignment_length' => '324',
			'identity_percentage' => '100.00',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0121G00040' => array(
			'gene_id' => 'ES0121G00040',
			'e_value' => '1e-58',
			'bit_score' => '200',
			'alignment_length' => '255',
			'identity_percentage' => '38.82',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP07G01900' => array(
			'gene_id' => 'TP07G01900',
			'e_value' => '1e-42',
			'bit_score' => '153',
			'alignment_length' => '229',
			'identity_percentage' => '42.36',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_12G00880' => array(
			'gene_id' => 'PTI_12G00880',
			'e_value' => '1e-37',
			'bit_score' => '148',
			'alignment_length' => '230',
			'identity_percentage' => '37.83',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0012G00100' => array(
			'gene_id' => 'AA0012G00100',
			'e_value' => '2e-37',
			'bit_score' => '139',
			'alignment_length' => '243',
			'identity_percentage' => '35.80',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G91850' => array(
			'gene_id' => 'CV00G91850',
			'e_value' => '4e-34',
			'bit_score' => '131',
			'alignment_length' => '233',
			'identity_percentage' => '35.62',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_001G03160' => array(
			'gene_id' => 'CNC64A_001G03160',
			'e_value' => '5e-34',
			'bit_score' => '133',
			'alignment_length' => '246',
			'identity_percentage' => '36.99',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'HE0000G06670' => array(
			'gene_id' => 'HE0000G06670',
			'e_value' => '5e-34',
			'bit_score' => '130',
			'alignment_length' => '211',
			'identity_percentage' => '36.49',
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.01g01950' => array(
			'gene_id' => 'RCC4223.01g01950',
			'e_value' => '3e-33',
			'bit_score' => '133',
			'alignment_length' => '313',
			'identity_percentage' => '33.23',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.07g03960' => array(
			'gene_id' => 'RCC4223.07g03960',
			'e_value' => '7e-33',
			'bit_score' => '129',
			'alignment_length' => '285',
			'identity_percentage' => '31.93',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G42800' => array(
			'gene_id' => 'PI00G42800',
			'e_value' => '1e-32',
			'bit_score' => '129',
			'alignment_length' => '320',
			'identity_percentage' => '29.69',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.03g08350' => array(
			'gene_id' => 'RCC4223.03g08350',
			'e_value' => '1e-31',
			'bit_score' => '125',
			'alignment_length' => '291',
			'identity_percentage' => '29.55',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_005G01530' => array(
			'gene_id' => 'CNC64A_005G01530',
			'e_value' => '2e-31',
			'bit_score' => '126',
			'alignment_length' => '235',
			'identity_percentage' => '34.47',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G18900' => array(
			'gene_id' => 'VC00G18900',
			'e_value' => '3e-31',
			'bit_score' => '125',
			'alignment_length' => '271',
			'identity_percentage' => '32.84',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G33460' => array(
			'gene_id' => 'PI00G33460',
			'e_value' => '1e-30',
			'bit_score' => '127',
			'alignment_length' => '271',
			'identity_percentage' => '33.21',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G18880' => array(
			'gene_id' => 'VC00G18880',
			'e_value' => '1e-30',
			'bit_score' => '122',
			'alignment_length' => '277',
			'identity_percentage' => '32.49',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G15880' => array(
			'gene_id' => 'PI00G15880',
			'e_value' => '1e-30',
			'bit_score' => '126',
			'alignment_length' => '262',
			'identity_percentage' => '33.21',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G29440' => array(
			'gene_id' => 'PI00G29440',
			'e_value' => '2e-30',
			'bit_score' => '122',
			'alignment_length' => '269',
			'identity_percentage' => '30.11',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.02g06100' => array(
			'gene_id' => 'RCC4223.02g06100',
			'e_value' => '2e-30',
			'bit_score' => '125',
			'alignment_length' => '262',
			'identity_percentage' => '32.44',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.03g07040' => array(
			'gene_id' => 'RCC4223.03g07040',
			'e_value' => '2e-30',
			'bit_score' => '122',
			'alignment_length' => '273',
			'identity_percentage' => '31.50',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G30540' => array(
			'gene_id' => 'PI00G30540',
			'e_value' => '8e-30',
			'bit_score' => '121',
			'alignment_length' => '286',
			'identity_percentage' => '31.47',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.01g05230' => array(
			'gene_id' => 'RCC4223.01g05230',
			'e_value' => '2e-29',
			'bit_score' => '120',
			'alignment_length' => '248',
			'identity_percentage' => '34.27',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G47900' => array(
			'gene_id' => 'PI00G47900',
			'e_value' => '2e-29',
			'bit_score' => '120',
			'alignment_length' => '248',
			'identity_percentage' => '34.27',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0011G02170' => array(
			'gene_id' => 'AA0011G02170',
			'e_value' => '7e-28',
			'bit_score' => '113',
			'alignment_length' => '200',
			'identity_percentage' => '35.50',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_009G00520' => array(
			'gene_id' => 'CNC64A_009G00520',
			'e_value' => '2e-27',
			'bit_score' => '113',
			'alignment_length' => '231',
			'identity_percentage' => '33.77',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0002G06930' => array(
			'gene_id' => 'AA0002G06930',
			'e_value' => '5e-27',
			'bit_score' => '112',
			'alignment_length' => '253',
			'identity_percentage' => '32.02',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_20G01150' => array(
			'gene_id' => 'PTI_20G01150',
			'e_value' => '9e-27',
			'bit_score' => '113',
			'alignment_length' => '214',
			'identity_percentage' => '35.05',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0059G00510' => array(
			'gene_id' => 'ES0059G00510',
			'e_value' => '4e-26',
			'bit_score' => '114',
			'alignment_length' => '145',
			'identity_percentage' => '42.07',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G23920' => array(
			'gene_id' => 'AP00G23920',
			'e_value' => '1e-25',
			'bit_score' => '108',
			'alignment_length' => '242',
			'identity_percentage' => '31.40',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G03960' => array(
			'gene_id' => 'PI00G03960',
			'e_value' => '8e-25',
			'bit_score' => '107',
			'alignment_length' => '291',
			'identity_percentage' => '30.58',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0017G01560' => array(
			'gene_id' => 'AA0017G01560',
			'e_value' => '2e-24',
			'bit_score' => '104',
			'alignment_length' => '210',
			'identity_percentage' => '33.33',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0280263' => array(
			'gene_id' => 'DDB_G0280263',
			'e_value' => '2e-24',
			'bit_score' => '104',
			'alignment_length' => '223',
			'identity_percentage' => '30.94',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0007G00910' => array(
			'gene_id' => 'AA0007G00910',
			'e_value' => '7e-24',
			'bit_score' => '102',
			'alignment_length' => '241',
			'identity_percentage' => '32.37',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh173790' => array(
			'gene_id' => 'emh173790',
			'e_value' => '6e-21',
			'bit_score' => '97.1',
			'alignment_length' => '269',
			'identity_percentage' => '32.34',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_019G01080' => array(
			'gene_id' => 'CNC64A_019G01080',
			'e_value' => '2e-20',
			'bit_score' => '95.9',
			'alignment_length' => '211',
			'identity_percentage' => '35.07',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0002G05820' => array(
			'gene_id' => 'AA0002G05820',
			'e_value' => '1e-19',
			'bit_score' => '90.9',
			'alignment_length' => '161',
			'identity_percentage' => '37.89',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh664230' => array(
			'gene_id' => 'emh664230',
			'e_value' => '3e-19',
			'bit_score' => '92.4',
			'alignment_length' => '234',
			'identity_percentage' => '32.05',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G42810' => array(
			'gene_id' => 'PI00G42810',
			'e_value' => '3e-19',
			'bit_score' => '90.5',
			'alignment_length' => '319',
			'identity_percentage' => '26.96',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh466680' => array(
			'gene_id' => 'emh466680',
			'e_value' => '1e-18',
			'bit_score' => '90.9',
			'alignment_length' => '259',
			'identity_percentage' => '30.50',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh62480' => array(
			'gene_id' => 'emh62480',
			'e_value' => '3e-18',
			'bit_score' => '89.7',
			'alignment_length' => '260',
			'identity_percentage' => '31.92',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh572420' => array(
			'gene_id' => 'emh572420',
			'e_value' => '4e-18',
			'bit_score' => '89.4',
			'alignment_length' => '260',
			'identity_percentage' => '31.92',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_081G00020' => array(
			'gene_id' => 'CNC64A_081G00020',
			'e_value' => '5e-18',
			'bit_score' => '85.1',
			'alignment_length' => '200',
			'identity_percentage' => '31.00',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100043g13' => array(
			'gene_id' => 'Naga_100043g13',
			'e_value' => '8e-18',
			'bit_score' => '87.8',
			'alignment_length' => '177',
			'identity_percentage' => '33.33',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_025G00190' => array(
			'gene_id' => 'CNC64A_025G00190',
			'e_value' => '1e-17',
			'bit_score' => '85.1',
			'alignment_length' => '200',
			'identity_percentage' => '31.00',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.07g03950' => array(
			'gene_id' => 'RCC4223.07g03950',
			'e_value' => '4e-17',
			'bit_score' => '84.7',
			'alignment_length' => '330',
			'identity_percentage' => '26.06',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR02G10720' => array(
			'gene_id' => 'CR02G10720',
			'e_value' => '1e-16',
			'bit_score' => '82.8',
			'alignment_length' => '278',
			'identity_percentage' => '27.34',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0002G05810' => array(
			'gene_id' => 'AA0002G05810',
			'e_value' => '2e-15',
			'bit_score' => '80.5',
			'alignment_length' => '60',
			'identity_percentage' => '58.33',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0263G00050' => array(
			'gene_id' => 'ES0263G00050',
			'e_value' => '2e-15',
			'bit_score' => '75.9',
			'alignment_length' => '91',
			'identity_percentage' => '42.86',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G65760' => array(
			'gene_id' => 'PI00G65760',
			'e_value' => '2e-15',
			'bit_score' => '79.7',
			'alignment_length' => '269',
			'identity_percentage' => '26.39',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OT_17G01960' => array(
			'gene_id' => 'OT_17G01960',
			'e_value' => '7e-15',
			'bit_score' => '79.0',
			'alignment_length' => '218',
			'identity_percentage' => '27.06',
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh349180' => array(
			'gene_id' => 'emh349180',
			'e_value' => '8e-15',
			'bit_score' => '76.6',
			'alignment_length' => '196',
			'identity_percentage' => '30.61',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR03G07040' => array(
			'gene_id' => 'CR03G07040',
			'e_value' => '2e-13',
			'bit_score' => '75.1',
			'alignment_length' => '272',
			'identity_percentage' => '28.68',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MRCC299_05G06940' => array(
			'gene_id' => 'MRCC299_05G06940',
			'e_value' => '1e-12',
			'bit_score' => '72.8',
			'alignment_length' => '252',
			'identity_percentage' => '29.76',
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR03G06520' => array(
			'gene_id' => 'CR03G06520',
			'e_value' => '1e-12',
			'bit_score' => '72.0',
			'alignment_length' => '180',
			'identity_percentage' => '29.44',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL16G02020' => array(
			'gene_id' => 'OL16G02020',
			'e_value' => '1e-09',
			'bit_score' => '62.8',
			'alignment_length' => '219',
			'identity_percentage' => '25.57',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ORCC809_16G00660' => array(
			'gene_id' => 'ORCC809_16G00660',
			'e_value' => '2e-09',
			'bit_score' => '62.4',
			'alignment_length' => '221',
			'identity_percentage' => '24.89',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0040321' => array(
			'gene_id' => 'FBgn0040321',
			'e_value' => '3e-08',
			'bit_score' => '58.9',
			'alignment_length' => '286',
			'identity_percentage' => '25.87',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0059G00670' => array(
			'gene_id' => 'ES0059G00670',
			'e_value' => '4e-08',
			'bit_score' => '54.7',
			'alignment_length' => '75',
			'identity_percentage' => '40.00',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh26090' => array(
			'gene_id' => 'emh26090',
			'e_value' => '6e-07',
			'bit_score' => '52.0',
			'alignment_length' => '111',
			'identity_percentage' => '33.33',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh55400' => array(
			'gene_id' => 'emh55400',
			'e_value' => '3e-06',
			'bit_score' => '52.4',
			'alignment_length' => '226',
			'identity_percentage' => '24.78',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'esi' => array(
			(int) 0 => 'ES0121G00230',
			(int) 1 => 'ES0121G00040',
			(int) 2 => 'ES0059G00510',
			(int) 3 => 'ES0263G00050',
			(int) 4 => 'ES0059G00670'
		),
		'tps' => array(
			(int) 0 => 'TP07G01900'
		),
		'ptri' => array(
			(int) 0 => 'PTI_12G00880',
			(int) 1 => 'PTI_20G01150'
		),
		'aan' => array(
			(int) 0 => 'AA0012G00100',
			(int) 1 => 'AA0011G02170',
			(int) 2 => 'AA0002G06930',
			(int) 3 => 'AA0017G01560',
			(int) 4 => 'AA0007G00910',
			(int) 5 => 'AA0002G05820',
			(int) 6 => 'AA0002G05810'
		),
		'cvu' => array(
			(int) 0 => 'CV00G91850'
		),
		'cnc64a' => array(
			(int) 0 => 'CNC64A_001G03160',
			(int) 1 => 'CNC64A_005G01530',
			(int) 2 => 'CNC64A_009G00520',
			(int) 3 => 'CNC64A_019G01080',
			(int) 4 => 'CNC64A_025G00190'
		),
		'hsp' => array(
			(int) 0 => 'HE0000G06670'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.01g01950',
			(int) 1 => 'RCC4223.07g03960',
			(int) 2 => 'RCC4223.03g08350',
			(int) 3 => 'RCC4223.02g06100',
			(int) 4 => 'RCC4223.03g07040',
			(int) 5 => 'RCC4223.01g05230',
			(int) 6 => 'RCC4223.07g03950'
		),
		'pse3' => array(
			(int) 0 => 'PI00G42800',
			(int) 1 => 'PI00G33460',
			(int) 2 => 'PI00G15880',
			(int) 3 => 'PI00G29440',
			(int) 4 => 'PI00G30540',
			(int) 5 => 'PI00G47900',
			(int) 6 => 'PI00G03960',
			(int) 7 => 'PI00G42810',
			(int) 8 => 'PI00G65760'
		),
		'vca' => array(
			(int) 0 => 'VC00G18900',
			(int) 1 => 'VC00G18880'
		),
		'apr' => array(
			(int) 0 => 'AP00G23920'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0280263'
		),
		'emh' => array(
			(int) 0 => 'emh173790',
			(int) 1 => 'emh664230',
			(int) 2 => 'emh466680',
			(int) 3 => 'emh62480',
			(int) 4 => 'emh572420',
			(int) 5 => 'emh349180',
			(int) 6 => 'emh26090',
			(int) 7 => 'emh55400'
		),
		'nga' => array(
			(int) 0 => 'Naga_100043g13'
		),
		'cre' => array(
			(int) 0 => 'CR02G10720',
			(int) 1 => 'CR03G07040',
			(int) 2 => 'CR03G06520'
		),
		'ota' => array(
			(int) 0 => 'OT_17G01960'
		),
		'mrcc299' => array(
			(int) 0 => 'MRCC299_05G06940'
		),
		'olu' => array(
			(int) 0 => 'OL16G02020'
		),
		'orcc809' => array(
			(int) 0 => 'ORCC809_16G00660'
		),
		'drm' => array(
			(int) 0 => 'FBgn0040321'
		)
	),
	'gene_id' => 'ES0121G00230',
	'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' => 'ES0121G00230',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'AT2G20410',
	'gf_placeholder' => 'HOM03P030720',
	'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(
	'ES0121G00230' => array(
		'gene_id' => 'ES0121G00230',
		'e_value' => '0.0',
		'bit_score' => '667',
		'alignment_length' => '324',
		'identity_percentage' => '100.00',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'ES0121G00040' => array(
		'gene_id' => 'ES0121G00040',
		'e_value' => '1e-58',
		'bit_score' => '200',
		'alignment_length' => '255',
		'identity_percentage' => '38.82',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'TP07G01900' => array(
		'gene_id' => 'TP07G01900',
		'e_value' => '1e-42',
		'bit_score' => '153',
		'alignment_length' => '229',
		'identity_percentage' => '42.36',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'PTI_12G00880' => array(
		'gene_id' => 'PTI_12G00880',
		'e_value' => '1e-37',
		'bit_score' => '148',
		'alignment_length' => '230',
		'identity_percentage' => '37.83',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'AA0012G00100' => array(
		'gene_id' => 'AA0012G00100',
		'e_value' => '2e-37',
		'bit_score' => '139',
		'alignment_length' => '243',
		'identity_percentage' => '35.80',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'CV00G91850' => array(
		'gene_id' => 'CV00G91850',
		'e_value' => '4e-34',
		'bit_score' => '131',
		'alignment_length' => '233',
		'identity_percentage' => '35.62',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'CNC64A_001G03160' => array(
		'gene_id' => 'CNC64A_001G03160',
		'e_value' => '5e-34',
		'bit_score' => '133',
		'alignment_length' => '246',
		'identity_percentage' => '36.99',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'HE0000G06670' => array(
		'gene_id' => 'HE0000G06670',
		'e_value' => '5e-34',
		'bit_score' => '130',
		'alignment_length' => '211',
		'identity_percentage' => '36.49',
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'RCC4223.01g01950' => array(
		'gene_id' => 'RCC4223.01g01950',
		'e_value' => '3e-33',
		'bit_score' => '133',
		'alignment_length' => '313',
		'identity_percentage' => '33.23',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P073173'
		)
	),
	'RCC4223.07g03960' => array(
		'gene_id' => 'RCC4223.07g03960',
		'e_value' => '7e-33',
		'bit_score' => '129',
		'alignment_length' => '285',
		'identity_percentage' => '31.93',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P063421'
		)
	),
	'PI00G42800' => array(
		'gene_id' => 'PI00G42800',
		'e_value' => '1e-32',
		'bit_score' => '129',
		'alignment_length' => '320',
		'identity_percentage' => '29.69',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P063421'
		)
	),
	'RCC4223.03g08350' => array(
		'gene_id' => 'RCC4223.03g08350',
		'e_value' => '1e-31',
		'bit_score' => '125',
		'alignment_length' => '291',
		'identity_percentage' => '29.55',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P033528'
		)
	),
	'CNC64A_005G01530' => array(
		'gene_id' => 'CNC64A_005G01530',
		'e_value' => '2e-31',
		'bit_score' => '126',
		'alignment_length' => '235',
		'identity_percentage' => '34.47',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'VC00G18900' => array(
		'gene_id' => 'VC00G18900',
		'e_value' => '3e-31',
		'bit_score' => '125',
		'alignment_length' => '271',
		'identity_percentage' => '32.84',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'PI00G33460' => array(
		'gene_id' => 'PI00G33460',
		'e_value' => '1e-30',
		'bit_score' => '127',
		'alignment_length' => '271',
		'identity_percentage' => '33.21',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P073173'
		)
	),
	'VC00G18880' => array(
		'gene_id' => 'VC00G18880',
		'e_value' => '1e-30',
		'bit_score' => '122',
		'alignment_length' => '277',
		'identity_percentage' => '32.49',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'PI00G15880' => array(
		'gene_id' => 'PI00G15880',
		'e_value' => '1e-30',
		'bit_score' => '126',
		'alignment_length' => '262',
		'identity_percentage' => '33.21',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P069125'
		)
	),
	'PI00G29440' => array(
		'gene_id' => 'PI00G29440',
		'e_value' => '2e-30',
		'bit_score' => '122',
		'alignment_length' => '269',
		'identity_percentage' => '30.11',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P033528'
		)
	),
	'RCC4223.02g06100' => array(
		'gene_id' => 'RCC4223.02g06100',
		'e_value' => '2e-30',
		'bit_score' => '125',
		'alignment_length' => '262',
		'identity_percentage' => '32.44',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P069125'
		)
	),
	'RCC4223.03g07040' => array(
		'gene_id' => 'RCC4223.03g07040',
		'e_value' => '2e-30',
		'bit_score' => '122',
		'alignment_length' => '273',
		'identity_percentage' => '31.50',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P069753'
		)
	),
	'PI00G30540' => array(
		'gene_id' => 'PI00G30540',
		'e_value' => '8e-30',
		'bit_score' => '121',
		'alignment_length' => '286',
		'identity_percentage' => '31.47',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P069753'
		)
	),
	'RCC4223.01g05230' => array(
		'gene_id' => 'RCC4223.01g05230',
		'e_value' => '2e-29',
		'bit_score' => '120',
		'alignment_length' => '248',
		'identity_percentage' => '34.27',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'PI00G47900' => array(
		'gene_id' => 'PI00G47900',
		'e_value' => '2e-29',
		'bit_score' => '120',
		'alignment_length' => '248',
		'identity_percentage' => '34.27',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'AA0011G02170' => array(
		'gene_id' => 'AA0011G02170',
		'e_value' => '7e-28',
		'bit_score' => '113',
		'alignment_length' => '200',
		'identity_percentage' => '35.50',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'CNC64A_009G00520' => array(
		'gene_id' => 'CNC64A_009G00520',
		'e_value' => '2e-27',
		'bit_score' => '113',
		'alignment_length' => '231',
		'identity_percentage' => '33.77',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P071593'
		)
	),
	'AA0002G06930' => array(
		'gene_id' => 'AA0002G06930',
		'e_value' => '5e-27',
		'bit_score' => '112',
		'alignment_length' => '253',
		'identity_percentage' => '32.02',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'PTI_20G01150' => array(
		'gene_id' => 'PTI_20G01150',
		'e_value' => '9e-27',
		'bit_score' => '113',
		'alignment_length' => '214',
		'identity_percentage' => '35.05',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P143054'
		)
	),
	'ES0059G00510' => array(
		'gene_id' => 'ES0059G00510',
		'e_value' => '4e-26',
		'bit_score' => '114',
		'alignment_length' => '145',
		'identity_percentage' => '42.07',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P071593'
		)
	),
	'AP00G23920' => array(
		'gene_id' => 'AP00G23920',
		'e_value' => '1e-25',
		'bit_score' => '108',
		'alignment_length' => '242',
		'identity_percentage' => '31.40',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'PI00G03960' => array(
		'gene_id' => 'PI00G03960',
		'e_value' => '8e-25',
		'bit_score' => '107',
		'alignment_length' => '291',
		'identity_percentage' => '30.58',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P096624'
		)
	),
	'AA0017G01560' => array(
		'gene_id' => 'AA0017G01560',
		'e_value' => '2e-24',
		'bit_score' => '104',
		'alignment_length' => '210',
		'identity_percentage' => '33.33',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'DDB_G0280263' => array(
		'gene_id' => 'DDB_G0280263',
		'e_value' => '2e-24',
		'bit_score' => '104',
		'alignment_length' => '223',
		'identity_percentage' => '30.94',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'AA0007G00910' => array(
		'gene_id' => 'AA0007G00910',
		'e_value' => '7e-24',
		'bit_score' => '102',
		'alignment_length' => '241',
		'identity_percentage' => '32.37',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'emh173790' => array(
		'gene_id' => 'emh173790',
		'e_value' => '6e-21',
		'bit_score' => '97.1',
		'alignment_length' => '269',
		'identity_percentage' => '32.34',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P049315'
		)
	),
	'CNC64A_019G01080' => array(
		'gene_id' => 'CNC64A_019G01080',
		'e_value' => '2e-20',
		'bit_score' => '95.9',
		'alignment_length' => '211',
		'identity_percentage' => '35.07',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'AA0002G05820' => array(
		'gene_id' => 'AA0002G05820',
		'e_value' => '1e-19',
		'bit_score' => '90.9',
		'alignment_length' => '161',
		'identity_percentage' => '37.89',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'emh664230' => array(
		'gene_id' => 'emh664230',
		'e_value' => '3e-19',
		'bit_score' => '92.4',
		'alignment_length' => '234',
		'identity_percentage' => '32.05',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P049315'
		)
	),
	'PI00G42810' => array(
		'gene_id' => 'PI00G42810',
		'e_value' => '3e-19',
		'bit_score' => '90.5',
		'alignment_length' => '319',
		'identity_percentage' => '26.96',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P062810'
		)
	),
	'emh466680' => array(
		'gene_id' => 'emh466680',
		'e_value' => '1e-18',
		'bit_score' => '90.9',
		'alignment_length' => '259',
		'identity_percentage' => '30.50',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'emh62480' => array(
		'gene_id' => 'emh62480',
		'e_value' => '3e-18',
		'bit_score' => '89.7',
		'alignment_length' => '260',
		'identity_percentage' => '31.92',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'emh572420' => array(
		'gene_id' => 'emh572420',
		'e_value' => '4e-18',
		'bit_score' => '89.4',
		'alignment_length' => '260',
		'identity_percentage' => '31.92',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'CNC64A_081G00020' => array(
		'gene_id' => 'CNC64A_081G00020',
		'e_value' => '5e-18',
		'bit_score' => '85.1',
		'alignment_length' => '200',
		'identity_percentage' => '31.00',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P047980'
		)
	),
	'Naga_100043g13' => array(
		'gene_id' => 'Naga_100043g13',
		'e_value' => '8e-18',
		'bit_score' => '87.8',
		'alignment_length' => '177',
		'identity_percentage' => '33.33',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'CNC64A_025G00190' => array(
		'gene_id' => 'CNC64A_025G00190',
		'e_value' => '1e-17',
		'bit_score' => '85.1',
		'alignment_length' => '200',
		'identity_percentage' => '31.00',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P047980'
		)
	),
	'RCC4223.07g03950' => array(
		'gene_id' => 'RCC4223.07g03950',
		'e_value' => '4e-17',
		'bit_score' => '84.7',
		'alignment_length' => '330',
		'identity_percentage' => '26.06',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P062810'
		)
	),
	'CR02G10720' => array(
		'gene_id' => 'CR02G10720',
		'e_value' => '1e-16',
		'bit_score' => '82.8',
		'alignment_length' => '278',
		'identity_percentage' => '27.34',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'AA0002G05810' => array(
		'gene_id' => 'AA0002G05810',
		'e_value' => '2e-15',
		'bit_score' => '80.5',
		'alignment_length' => '60',
		'identity_percentage' => '58.33',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'ES0263G00050' => array(
		'gene_id' => 'ES0263G00050',
		'e_value' => '2e-15',
		'bit_score' => '75.9',
		'alignment_length' => '91',
		'identity_percentage' => '42.86',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'PI00G65760' => array(
		'gene_id' => 'PI00G65760',
		'e_value' => '2e-15',
		'bit_score' => '79.7',
		'alignment_length' => '269',
		'identity_percentage' => '26.39',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P130752'
		)
	),
	'OT_17G01960' => array(
		'gene_id' => 'OT_17G01960',
		'e_value' => '7e-15',
		'bit_score' => '79.0',
		'alignment_length' => '218',
		'identity_percentage' => '27.06',
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'gf' => array(
			'HOMFAM' => 'HOM03P012932',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'emh349180' => array(
		'gene_id' => 'emh349180',
		'e_value' => '8e-15',
		'bit_score' => '76.6',
		'alignment_length' => '196',
		'identity_percentage' => '30.61',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P113167'
		)
	),
	'CR03G07040' => array(
		'gene_id' => 'CR03G07040',
		'e_value' => '2e-13',
		'bit_score' => '75.1',
		'alignment_length' => '272',
		'identity_percentage' => '28.68',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'MRCC299_05G06940' => array(
		'gene_id' => 'MRCC299_05G06940',
		'e_value' => '1e-12',
		'bit_score' => '72.8',
		'alignment_length' => '252',
		'identity_percentage' => '29.76',
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'gf' => array(
			'HOMFAM' => 'HOM03P012932',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'CR03G06520' => array(
		'gene_id' => 'CR03G06520',
		'e_value' => '1e-12',
		'bit_score' => '72.0',
		'alignment_length' => '180',
		'identity_percentage' => '29.44',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P033528'
		)
	),
	'OL16G02020' => array(
		'gene_id' => 'OL16G02020',
		'e_value' => '1e-09',
		'bit_score' => '62.8',
		'alignment_length' => '219',
		'identity_percentage' => '25.57',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P012932',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'ORCC809_16G00660' => array(
		'gene_id' => 'ORCC809_16G00660',
		'e_value' => '2e-09',
		'bit_score' => '62.4',
		'alignment_length' => '221',
		'identity_percentage' => '24.89',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P012932',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'FBgn0040321' => array(
		'gene_id' => 'FBgn0040321',
		'e_value' => '3e-08',
		'bit_score' => '58.9',
		'alignment_length' => '286',
		'identity_percentage' => '25.87',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P012272',
			'ORTHOFAM' => 'ORTHO03P022962'
		)
	),
	'ES0059G00670' => array(
		'gene_id' => 'ES0059G00670',
		'e_value' => '4e-08',
		'bit_score' => '54.7',
		'alignment_length' => '75',
		'identity_percentage' => '40.00',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P135554'
		)
	),
	'emh26090' => array(
		'gene_id' => 'emh26090',
		'e_value' => '6e-07',
		'bit_score' => '52.0',
		'alignment_length' => '111',
		'identity_percentage' => '33.33',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P109773'
		)
	),
	'emh55400' => array(
		'gene_id' => 'emh55400',
		'e_value' => '3e-06',
		'bit_score' => '52.4',
		'alignment_length' => '226',
		'identity_percentage' => '24.78',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P015309',
			'ORTHOFAM' => 'ORTHO03P034004'
		)
	)
)
$similarity_hits_species = array(
	'esi' => array(
		(int) 0 => 'ES0121G00230',
		(int) 1 => 'ES0121G00040',
		(int) 2 => 'ES0059G00510',
		(int) 3 => 'ES0263G00050',
		(int) 4 => 'ES0059G00670'
	),
	'tps' => array(
		(int) 0 => 'TP07G01900'
	),
	'ptri' => array(
		(int) 0 => 'PTI_12G00880',
		(int) 1 => 'PTI_20G01150'
	),
	'aan' => array(
		(int) 0 => 'AA0012G00100',
		(int) 1 => 'AA0011G02170',
		(int) 2 => 'AA0002G06930',
		(int) 3 => 'AA0017G01560',
		(int) 4 => 'AA0007G00910',
		(int) 5 => 'AA0002G05820',
		(int) 6 => 'AA0002G05810'
	),
	'cvu' => array(
		(int) 0 => 'CV00G91850'
	),
	'cnc64a' => array(
		(int) 0 => 'CNC64A_001G03160',
		(int) 1 => 'CNC64A_005G01530',
		(int) 2 => 'CNC64A_009G00520',
		(int) 3 => 'CNC64A_019G01080',
		(int) 4 => 'CNC64A_025G00190'
	),
	'hsp' => array(
		(int) 0 => 'HE0000G06670'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.01g01950',
		(int) 1 => 'RCC4223.07g03960',
		(int) 2 => 'RCC4223.03g08350',
		(int) 3 => 'RCC4223.02g06100',
		(int) 4 => 'RCC4223.03g07040',
		(int) 5 => 'RCC4223.01g05230',
		(int) 6 => 'RCC4223.07g03950'
	),
	'pse3' => array(
		(int) 0 => 'PI00G42800',
		(int) 1 => 'PI00G33460',
		(int) 2 => 'PI00G15880',
		(int) 3 => 'PI00G29440',
		(int) 4 => 'PI00G30540',
		(int) 5 => 'PI00G47900',
		(int) 6 => 'PI00G03960',
		(int) 7 => 'PI00G42810',
		(int) 8 => 'PI00G65760'
	),
	'vca' => array(
		(int) 0 => 'VC00G18900',
		(int) 1 => 'VC00G18880'
	),
	'apr' => array(
		(int) 0 => 'AP00G23920'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0280263'
	),
	'emh' => array(
		(int) 0 => 'emh173790',
		(int) 1 => 'emh664230',
		(int) 2 => 'emh466680',
		(int) 3 => 'emh62480',
		(int) 4 => 'emh572420',
		(int) 5 => 'emh349180',
		(int) 6 => 'emh26090',
		(int) 7 => 'emh55400'
	),
	'nga' => array(
		(int) 0 => 'Naga_100043g13'
	),
	'cre' => array(
		(int) 0 => 'CR02G10720',
		(int) 1 => 'CR03G07040',
		(int) 2 => 'CR03G06520'
	),
	'ota' => array(
		(int) 0 => 'OT_17G01960'
	),
	'mrcc299' => array(
		(int) 0 => 'MRCC299_05G06940'
	),
	'olu' => array(
		(int) 0 => 'OL16G02020'
	),
	'orcc809' => array(
		(int) 0 => 'ORCC809_16G00660'
	),
	'drm' => array(
		(int) 0 => 'FBgn0040321'
	)
)
$gene_id = 'ES0121G00230'
$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 = 'ES0121G00230'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'AT2G20410'
$gf_placeholder = 'HOM03P030720'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_081G00020',
	'e_value' => '5e-18',
	'bit_score' => '85.1',
	'alignment_length' => '200',
	'identity_percentage' => '31.00',
	'gf' => array(
		'HOMFAM' => 'HOM03P001374',
		'ORTHOFAM' => 'ORTHO03P047980'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_081G00020'
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(
		'ES0121G00230' => array(
			'gene_id' => 'ES0121G00230',
			'e_value' => '0.0',
			'bit_score' => '667',
			'alignment_length' => '324',
			'identity_percentage' => '100.00',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0121G00040' => array(
			'gene_id' => 'ES0121G00040',
			'e_value' => '1e-58',
			'bit_score' => '200',
			'alignment_length' => '255',
			'identity_percentage' => '38.82',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP07G01900' => array(
			'gene_id' => 'TP07G01900',
			'e_value' => '1e-42',
			'bit_score' => '153',
			'alignment_length' => '229',
			'identity_percentage' => '42.36',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_12G00880' => array(
			'gene_id' => 'PTI_12G00880',
			'e_value' => '1e-37',
			'bit_score' => '148',
			'alignment_length' => '230',
			'identity_percentage' => '37.83',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0012G00100' => array(
			'gene_id' => 'AA0012G00100',
			'e_value' => '2e-37',
			'bit_score' => '139',
			'alignment_length' => '243',
			'identity_percentage' => '35.80',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G91850' => array(
			'gene_id' => 'CV00G91850',
			'e_value' => '4e-34',
			'bit_score' => '131',
			'alignment_length' => '233',
			'identity_percentage' => '35.62',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_001G03160' => array(
			'gene_id' => 'CNC64A_001G03160',
			'e_value' => '5e-34',
			'bit_score' => '133',
			'alignment_length' => '246',
			'identity_percentage' => '36.99',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'HE0000G06670' => array(
			'gene_id' => 'HE0000G06670',
			'e_value' => '5e-34',
			'bit_score' => '130',
			'alignment_length' => '211',
			'identity_percentage' => '36.49',
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.01g01950' => array(
			'gene_id' => 'RCC4223.01g01950',
			'e_value' => '3e-33',
			'bit_score' => '133',
			'alignment_length' => '313',
			'identity_percentage' => '33.23',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.07g03960' => array(
			'gene_id' => 'RCC4223.07g03960',
			'e_value' => '7e-33',
			'bit_score' => '129',
			'alignment_length' => '285',
			'identity_percentage' => '31.93',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G42800' => array(
			'gene_id' => 'PI00G42800',
			'e_value' => '1e-32',
			'bit_score' => '129',
			'alignment_length' => '320',
			'identity_percentage' => '29.69',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.03g08350' => array(
			'gene_id' => 'RCC4223.03g08350',
			'e_value' => '1e-31',
			'bit_score' => '125',
			'alignment_length' => '291',
			'identity_percentage' => '29.55',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_005G01530' => array(
			'gene_id' => 'CNC64A_005G01530',
			'e_value' => '2e-31',
			'bit_score' => '126',
			'alignment_length' => '235',
			'identity_percentage' => '34.47',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G18900' => array(
			'gene_id' => 'VC00G18900',
			'e_value' => '3e-31',
			'bit_score' => '125',
			'alignment_length' => '271',
			'identity_percentage' => '32.84',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G33460' => array(
			'gene_id' => 'PI00G33460',
			'e_value' => '1e-30',
			'bit_score' => '127',
			'alignment_length' => '271',
			'identity_percentage' => '33.21',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G18880' => array(
			'gene_id' => 'VC00G18880',
			'e_value' => '1e-30',
			'bit_score' => '122',
			'alignment_length' => '277',
			'identity_percentage' => '32.49',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G15880' => array(
			'gene_id' => 'PI00G15880',
			'e_value' => '1e-30',
			'bit_score' => '126',
			'alignment_length' => '262',
			'identity_percentage' => '33.21',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G29440' => array(
			'gene_id' => 'PI00G29440',
			'e_value' => '2e-30',
			'bit_score' => '122',
			'alignment_length' => '269',
			'identity_percentage' => '30.11',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.02g06100' => array(
			'gene_id' => 'RCC4223.02g06100',
			'e_value' => '2e-30',
			'bit_score' => '125',
			'alignment_length' => '262',
			'identity_percentage' => '32.44',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.03g07040' => array(
			'gene_id' => 'RCC4223.03g07040',
			'e_value' => '2e-30',
			'bit_score' => '122',
			'alignment_length' => '273',
			'identity_percentage' => '31.50',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G30540' => array(
			'gene_id' => 'PI00G30540',
			'e_value' => '8e-30',
			'bit_score' => '121',
			'alignment_length' => '286',
			'identity_percentage' => '31.47',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.01g05230' => array(
			'gene_id' => 'RCC4223.01g05230',
			'e_value' => '2e-29',
			'bit_score' => '120',
			'alignment_length' => '248',
			'identity_percentage' => '34.27',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G47900' => array(
			'gene_id' => 'PI00G47900',
			'e_value' => '2e-29',
			'bit_score' => '120',
			'alignment_length' => '248',
			'identity_percentage' => '34.27',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0011G02170' => array(
			'gene_id' => 'AA0011G02170',
			'e_value' => '7e-28',
			'bit_score' => '113',
			'alignment_length' => '200',
			'identity_percentage' => '35.50',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_009G00520' => array(
			'gene_id' => 'CNC64A_009G00520',
			'e_value' => '2e-27',
			'bit_score' => '113',
			'alignment_length' => '231',
			'identity_percentage' => '33.77',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0002G06930' => array(
			'gene_id' => 'AA0002G06930',
			'e_value' => '5e-27',
			'bit_score' => '112',
			'alignment_length' => '253',
			'identity_percentage' => '32.02',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_20G01150' => array(
			'gene_id' => 'PTI_20G01150',
			'e_value' => '9e-27',
			'bit_score' => '113',
			'alignment_length' => '214',
			'identity_percentage' => '35.05',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0059G00510' => array(
			'gene_id' => 'ES0059G00510',
			'e_value' => '4e-26',
			'bit_score' => '114',
			'alignment_length' => '145',
			'identity_percentage' => '42.07',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G23920' => array(
			'gene_id' => 'AP00G23920',
			'e_value' => '1e-25',
			'bit_score' => '108',
			'alignment_length' => '242',
			'identity_percentage' => '31.40',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G03960' => array(
			'gene_id' => 'PI00G03960',
			'e_value' => '8e-25',
			'bit_score' => '107',
			'alignment_length' => '291',
			'identity_percentage' => '30.58',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0017G01560' => array(
			'gene_id' => 'AA0017G01560',
			'e_value' => '2e-24',
			'bit_score' => '104',
			'alignment_length' => '210',
			'identity_percentage' => '33.33',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0280263' => array(
			'gene_id' => 'DDB_G0280263',
			'e_value' => '2e-24',
			'bit_score' => '104',
			'alignment_length' => '223',
			'identity_percentage' => '30.94',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0007G00910' => array(
			'gene_id' => 'AA0007G00910',
			'e_value' => '7e-24',
			'bit_score' => '102',
			'alignment_length' => '241',
			'identity_percentage' => '32.37',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh173790' => array(
			'gene_id' => 'emh173790',
			'e_value' => '6e-21',
			'bit_score' => '97.1',
			'alignment_length' => '269',
			'identity_percentage' => '32.34',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_019G01080' => array(
			'gene_id' => 'CNC64A_019G01080',
			'e_value' => '2e-20',
			'bit_score' => '95.9',
			'alignment_length' => '211',
			'identity_percentage' => '35.07',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0002G05820' => array(
			'gene_id' => 'AA0002G05820',
			'e_value' => '1e-19',
			'bit_score' => '90.9',
			'alignment_length' => '161',
			'identity_percentage' => '37.89',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh664230' => array(
			'gene_id' => 'emh664230',
			'e_value' => '3e-19',
			'bit_score' => '92.4',
			'alignment_length' => '234',
			'identity_percentage' => '32.05',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G42810' => array(
			'gene_id' => 'PI00G42810',
			'e_value' => '3e-19',
			'bit_score' => '90.5',
			'alignment_length' => '319',
			'identity_percentage' => '26.96',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh466680' => array(
			'gene_id' => 'emh466680',
			'e_value' => '1e-18',
			'bit_score' => '90.9',
			'alignment_length' => '259',
			'identity_percentage' => '30.50',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh62480' => array(
			'gene_id' => 'emh62480',
			'e_value' => '3e-18',
			'bit_score' => '89.7',
			'alignment_length' => '260',
			'identity_percentage' => '31.92',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh572420' => array(
			'gene_id' => 'emh572420',
			'e_value' => '4e-18',
			'bit_score' => '89.4',
			'alignment_length' => '260',
			'identity_percentage' => '31.92',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_081G00020' => array(
			'gene_id' => 'CNC64A_081G00020',
			'e_value' => '5e-18',
			'bit_score' => '85.1',
			'alignment_length' => '200',
			'identity_percentage' => '31.00',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100043g13' => array(
			'gene_id' => 'Naga_100043g13',
			'e_value' => '8e-18',
			'bit_score' => '87.8',
			'alignment_length' => '177',
			'identity_percentage' => '33.33',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_025G00190' => array(
			'gene_id' => 'CNC64A_025G00190',
			'e_value' => '1e-17',
			'bit_score' => '85.1',
			'alignment_length' => '200',
			'identity_percentage' => '31.00',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.07g03950' => array(
			'gene_id' => 'RCC4223.07g03950',
			'e_value' => '4e-17',
			'bit_score' => '84.7',
			'alignment_length' => '330',
			'identity_percentage' => '26.06',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR02G10720' => array(
			'gene_id' => 'CR02G10720',
			'e_value' => '1e-16',
			'bit_score' => '82.8',
			'alignment_length' => '278',
			'identity_percentage' => '27.34',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0002G05810' => array(
			'gene_id' => 'AA0002G05810',
			'e_value' => '2e-15',
			'bit_score' => '80.5',
			'alignment_length' => '60',
			'identity_percentage' => '58.33',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0263G00050' => array(
			'gene_id' => 'ES0263G00050',
			'e_value' => '2e-15',
			'bit_score' => '75.9',
			'alignment_length' => '91',
			'identity_percentage' => '42.86',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G65760' => array(
			'gene_id' => 'PI00G65760',
			'e_value' => '2e-15',
			'bit_score' => '79.7',
			'alignment_length' => '269',
			'identity_percentage' => '26.39',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OT_17G01960' => array(
			'gene_id' => 'OT_17G01960',
			'e_value' => '7e-15',
			'bit_score' => '79.0',
			'alignment_length' => '218',
			'identity_percentage' => '27.06',
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh349180' => array(
			'gene_id' => 'emh349180',
			'e_value' => '8e-15',
			'bit_score' => '76.6',
			'alignment_length' => '196',
			'identity_percentage' => '30.61',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR03G07040' => array(
			'gene_id' => 'CR03G07040',
			'e_value' => '2e-13',
			'bit_score' => '75.1',
			'alignment_length' => '272',
			'identity_percentage' => '28.68',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MRCC299_05G06940' => array(
			'gene_id' => 'MRCC299_05G06940',
			'e_value' => '1e-12',
			'bit_score' => '72.8',
			'alignment_length' => '252',
			'identity_percentage' => '29.76',
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR03G06520' => array(
			'gene_id' => 'CR03G06520',
			'e_value' => '1e-12',
			'bit_score' => '72.0',
			'alignment_length' => '180',
			'identity_percentage' => '29.44',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL16G02020' => array(
			'gene_id' => 'OL16G02020',
			'e_value' => '1e-09',
			'bit_score' => '62.8',
			'alignment_length' => '219',
			'identity_percentage' => '25.57',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ORCC809_16G00660' => array(
			'gene_id' => 'ORCC809_16G00660',
			'e_value' => '2e-09',
			'bit_score' => '62.4',
			'alignment_length' => '221',
			'identity_percentage' => '24.89',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0040321' => array(
			'gene_id' => 'FBgn0040321',
			'e_value' => '3e-08',
			'bit_score' => '58.9',
			'alignment_length' => '286',
			'identity_percentage' => '25.87',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0059G00670' => array(
			'gene_id' => 'ES0059G00670',
			'e_value' => '4e-08',
			'bit_score' => '54.7',
			'alignment_length' => '75',
			'identity_percentage' => '40.00',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh26090' => array(
			'gene_id' => 'emh26090',
			'e_value' => '6e-07',
			'bit_score' => '52.0',
			'alignment_length' => '111',
			'identity_percentage' => '33.33',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh55400' => array(
			'gene_id' => 'emh55400',
			'e_value' => '3e-06',
			'bit_score' => '52.4',
			'alignment_length' => '226',
			'identity_percentage' => '24.78',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'esi' => array(
			(int) 0 => 'ES0121G00230',
			(int) 1 => 'ES0121G00040',
			(int) 2 => 'ES0059G00510',
			(int) 3 => 'ES0263G00050',
			(int) 4 => 'ES0059G00670'
		),
		'tps' => array(
			(int) 0 => 'TP07G01900'
		),
		'ptri' => array(
			(int) 0 => 'PTI_12G00880',
			(int) 1 => 'PTI_20G01150'
		),
		'aan' => array(
			(int) 0 => 'AA0012G00100',
			(int) 1 => 'AA0011G02170',
			(int) 2 => 'AA0002G06930',
			(int) 3 => 'AA0017G01560',
			(int) 4 => 'AA0007G00910',
			(int) 5 => 'AA0002G05820',
			(int) 6 => 'AA0002G05810'
		),
		'cvu' => array(
			(int) 0 => 'CV00G91850'
		),
		'cnc64a' => array(
			(int) 0 => 'CNC64A_001G03160',
			(int) 1 => 'CNC64A_005G01530',
			(int) 2 => 'CNC64A_009G00520',
			(int) 3 => 'CNC64A_019G01080',
			(int) 4 => 'CNC64A_025G00190'
		),
		'hsp' => array(
			(int) 0 => 'HE0000G06670'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.01g01950',
			(int) 1 => 'RCC4223.07g03960',
			(int) 2 => 'RCC4223.03g08350',
			(int) 3 => 'RCC4223.02g06100',
			(int) 4 => 'RCC4223.03g07040',
			(int) 5 => 'RCC4223.01g05230',
			(int) 6 => 'RCC4223.07g03950'
		),
		'pse3' => array(
			(int) 0 => 'PI00G42800',
			(int) 1 => 'PI00G33460',
			(int) 2 => 'PI00G15880',
			(int) 3 => 'PI00G29440',
			(int) 4 => 'PI00G30540',
			(int) 5 => 'PI00G47900',
			(int) 6 => 'PI00G03960',
			(int) 7 => 'PI00G42810',
			(int) 8 => 'PI00G65760'
		),
		'vca' => array(
			(int) 0 => 'VC00G18900',
			(int) 1 => 'VC00G18880'
		),
		'apr' => array(
			(int) 0 => 'AP00G23920'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0280263'
		),
		'emh' => array(
			(int) 0 => 'emh173790',
			(int) 1 => 'emh664230',
			(int) 2 => 'emh466680',
			(int) 3 => 'emh62480',
			(int) 4 => 'emh572420',
			(int) 5 => 'emh349180',
			(int) 6 => 'emh26090',
			(int) 7 => 'emh55400'
		),
		'nga' => array(
			(int) 0 => 'Naga_100043g13'
		),
		'cre' => array(
			(int) 0 => 'CR02G10720',
			(int) 1 => 'CR03G07040',
			(int) 2 => 'CR03G06520'
		),
		'ota' => array(
			(int) 0 => 'OT_17G01960'
		),
		'mrcc299' => array(
			(int) 0 => 'MRCC299_05G06940'
		),
		'olu' => array(
			(int) 0 => 'OL16G02020'
		),
		'orcc809' => array(
			(int) 0 => 'ORCC809_16G00660'
		),
		'drm' => array(
			(int) 0 => 'FBgn0040321'
		)
	),
	'gene_id' => 'ES0121G00230',
	'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' => 'ES0121G00230',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'AT2G20410',
	'gf_placeholder' => 'HOM03P030720',
	'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(
	'ES0121G00230' => array(
		'gene_id' => 'ES0121G00230',
		'e_value' => '0.0',
		'bit_score' => '667',
		'alignment_length' => '324',
		'identity_percentage' => '100.00',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'ES0121G00040' => array(
		'gene_id' => 'ES0121G00040',
		'e_value' => '1e-58',
		'bit_score' => '200',
		'alignment_length' => '255',
		'identity_percentage' => '38.82',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'TP07G01900' => array(
		'gene_id' => 'TP07G01900',
		'e_value' => '1e-42',
		'bit_score' => '153',
		'alignment_length' => '229',
		'identity_percentage' => '42.36',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'PTI_12G00880' => array(
		'gene_id' => 'PTI_12G00880',
		'e_value' => '1e-37',
		'bit_score' => '148',
		'alignment_length' => '230',
		'identity_percentage' => '37.83',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'AA0012G00100' => array(
		'gene_id' => 'AA0012G00100',
		'e_value' => '2e-37',
		'bit_score' => '139',
		'alignment_length' => '243',
		'identity_percentage' => '35.80',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'CV00G91850' => array(
		'gene_id' => 'CV00G91850',
		'e_value' => '4e-34',
		'bit_score' => '131',
		'alignment_length' => '233',
		'identity_percentage' => '35.62',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'CNC64A_001G03160' => array(
		'gene_id' => 'CNC64A_001G03160',
		'e_value' => '5e-34',
		'bit_score' => '133',
		'alignment_length' => '246',
		'identity_percentage' => '36.99',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'HE0000G06670' => array(
		'gene_id' => 'HE0000G06670',
		'e_value' => '5e-34',
		'bit_score' => '130',
		'alignment_length' => '211',
		'identity_percentage' => '36.49',
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'RCC4223.01g01950' => array(
		'gene_id' => 'RCC4223.01g01950',
		'e_value' => '3e-33',
		'bit_score' => '133',
		'alignment_length' => '313',
		'identity_percentage' => '33.23',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P073173'
		)
	),
	'RCC4223.07g03960' => array(
		'gene_id' => 'RCC4223.07g03960',
		'e_value' => '7e-33',
		'bit_score' => '129',
		'alignment_length' => '285',
		'identity_percentage' => '31.93',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P063421'
		)
	),
	'PI00G42800' => array(
		'gene_id' => 'PI00G42800',
		'e_value' => '1e-32',
		'bit_score' => '129',
		'alignment_length' => '320',
		'identity_percentage' => '29.69',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P063421'
		)
	),
	'RCC4223.03g08350' => array(
		'gene_id' => 'RCC4223.03g08350',
		'e_value' => '1e-31',
		'bit_score' => '125',
		'alignment_length' => '291',
		'identity_percentage' => '29.55',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P033528'
		)
	),
	'CNC64A_005G01530' => array(
		'gene_id' => 'CNC64A_005G01530',
		'e_value' => '2e-31',
		'bit_score' => '126',
		'alignment_length' => '235',
		'identity_percentage' => '34.47',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'VC00G18900' => array(
		'gene_id' => 'VC00G18900',
		'e_value' => '3e-31',
		'bit_score' => '125',
		'alignment_length' => '271',
		'identity_percentage' => '32.84',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'PI00G33460' => array(
		'gene_id' => 'PI00G33460',
		'e_value' => '1e-30',
		'bit_score' => '127',
		'alignment_length' => '271',
		'identity_percentage' => '33.21',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P073173'
		)
	),
	'VC00G18880' => array(
		'gene_id' => 'VC00G18880',
		'e_value' => '1e-30',
		'bit_score' => '122',
		'alignment_length' => '277',
		'identity_percentage' => '32.49',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'PI00G15880' => array(
		'gene_id' => 'PI00G15880',
		'e_value' => '1e-30',
		'bit_score' => '126',
		'alignment_length' => '262',
		'identity_percentage' => '33.21',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P069125'
		)
	),
	'PI00G29440' => array(
		'gene_id' => 'PI00G29440',
		'e_value' => '2e-30',
		'bit_score' => '122',
		'alignment_length' => '269',
		'identity_percentage' => '30.11',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P033528'
		)
	),
	'RCC4223.02g06100' => array(
		'gene_id' => 'RCC4223.02g06100',
		'e_value' => '2e-30',
		'bit_score' => '125',
		'alignment_length' => '262',
		'identity_percentage' => '32.44',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P069125'
		)
	),
	'RCC4223.03g07040' => array(
		'gene_id' => 'RCC4223.03g07040',
		'e_value' => '2e-30',
		'bit_score' => '122',
		'alignment_length' => '273',
		'identity_percentage' => '31.50',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P069753'
		)
	),
	'PI00G30540' => array(
		'gene_id' => 'PI00G30540',
		'e_value' => '8e-30',
		'bit_score' => '121',
		'alignment_length' => '286',
		'identity_percentage' => '31.47',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P069753'
		)
	),
	'RCC4223.01g05230' => array(
		'gene_id' => 'RCC4223.01g05230',
		'e_value' => '2e-29',
		'bit_score' => '120',
		'alignment_length' => '248',
		'identity_percentage' => '34.27',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'PI00G47900' => array(
		'gene_id' => 'PI00G47900',
		'e_value' => '2e-29',
		'bit_score' => '120',
		'alignment_length' => '248',
		'identity_percentage' => '34.27',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'AA0011G02170' => array(
		'gene_id' => 'AA0011G02170',
		'e_value' => '7e-28',
		'bit_score' => '113',
		'alignment_length' => '200',
		'identity_percentage' => '35.50',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'CNC64A_009G00520' => array(
		'gene_id' => 'CNC64A_009G00520',
		'e_value' => '2e-27',
		'bit_score' => '113',
		'alignment_length' => '231',
		'identity_percentage' => '33.77',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P071593'
		)
	),
	'AA0002G06930' => array(
		'gene_id' => 'AA0002G06930',
		'e_value' => '5e-27',
		'bit_score' => '112',
		'alignment_length' => '253',
		'identity_percentage' => '32.02',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'PTI_20G01150' => array(
		'gene_id' => 'PTI_20G01150',
		'e_value' => '9e-27',
		'bit_score' => '113',
		'alignment_length' => '214',
		'identity_percentage' => '35.05',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P143054'
		)
	),
	'ES0059G00510' => array(
		'gene_id' => 'ES0059G00510',
		'e_value' => '4e-26',
		'bit_score' => '114',
		'alignment_length' => '145',
		'identity_percentage' => '42.07',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P071593'
		)
	),
	'AP00G23920' => array(
		'gene_id' => 'AP00G23920',
		'e_value' => '1e-25',
		'bit_score' => '108',
		'alignment_length' => '242',
		'identity_percentage' => '31.40',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'PI00G03960' => array(
		'gene_id' => 'PI00G03960',
		'e_value' => '8e-25',
		'bit_score' => '107',
		'alignment_length' => '291',
		'identity_percentage' => '30.58',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P096624'
		)
	),
	'AA0017G01560' => array(
		'gene_id' => 'AA0017G01560',
		'e_value' => '2e-24',
		'bit_score' => '104',
		'alignment_length' => '210',
		'identity_percentage' => '33.33',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'DDB_G0280263' => array(
		'gene_id' => 'DDB_G0280263',
		'e_value' => '2e-24',
		'bit_score' => '104',
		'alignment_length' => '223',
		'identity_percentage' => '30.94',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'AA0007G00910' => array(
		'gene_id' => 'AA0007G00910',
		'e_value' => '7e-24',
		'bit_score' => '102',
		'alignment_length' => '241',
		'identity_percentage' => '32.37',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'emh173790' => array(
		'gene_id' => 'emh173790',
		'e_value' => '6e-21',
		'bit_score' => '97.1',
		'alignment_length' => '269',
		'identity_percentage' => '32.34',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P049315'
		)
	),
	'CNC64A_019G01080' => array(
		'gene_id' => 'CNC64A_019G01080',
		'e_value' => '2e-20',
		'bit_score' => '95.9',
		'alignment_length' => '211',
		'identity_percentage' => '35.07',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'AA0002G05820' => array(
		'gene_id' => 'AA0002G05820',
		'e_value' => '1e-19',
		'bit_score' => '90.9',
		'alignment_length' => '161',
		'identity_percentage' => '37.89',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'emh664230' => array(
		'gene_id' => 'emh664230',
		'e_value' => '3e-19',
		'bit_score' => '92.4',
		'alignment_length' => '234',
		'identity_percentage' => '32.05',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P049315'
		)
	),
	'PI00G42810' => array(
		'gene_id' => 'PI00G42810',
		'e_value' => '3e-19',
		'bit_score' => '90.5',
		'alignment_length' => '319',
		'identity_percentage' => '26.96',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P062810'
		)
	),
	'emh466680' => array(
		'gene_id' => 'emh466680',
		'e_value' => '1e-18',
		'bit_score' => '90.9',
		'alignment_length' => '259',
		'identity_percentage' => '30.50',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'emh62480' => array(
		'gene_id' => 'emh62480',
		'e_value' => '3e-18',
		'bit_score' => '89.7',
		'alignment_length' => '260',
		'identity_percentage' => '31.92',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'emh572420' => array(
		'gene_id' => 'emh572420',
		'e_value' => '4e-18',
		'bit_score' => '89.4',
		'alignment_length' => '260',
		'identity_percentage' => '31.92',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P006964',
			'ORTHOFAM' => 'ORTHO03P006259'
		)
	),
	'CNC64A_081G00020' => array(
		'gene_id' => 'CNC64A_081G00020',
		'e_value' => '5e-18',
		'bit_score' => '85.1',
		'alignment_length' => '200',
		'identity_percentage' => '31.00',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P047980'
		)
	),
	'Naga_100043g13' => array(
		'gene_id' => 'Naga_100043g13',
		'e_value' => '8e-18',
		'bit_score' => '87.8',
		'alignment_length' => '177',
		'identity_percentage' => '33.33',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'CNC64A_025G00190' => array(
		'gene_id' => 'CNC64A_025G00190',
		'e_value' => '1e-17',
		'bit_score' => '85.1',
		'alignment_length' => '200',
		'identity_percentage' => '31.00',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P047980'
		)
	),
	'RCC4223.07g03950' => array(
		'gene_id' => 'RCC4223.07g03950',
		'e_value' => '4e-17',
		'bit_score' => '84.7',
		'alignment_length' => '330',
		'identity_percentage' => '26.06',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P062810'
		)
	),
	'CR02G10720' => array(
		'gene_id' => 'CR02G10720',
		'e_value' => '1e-16',
		'bit_score' => '82.8',
		'alignment_length' => '278',
		'identity_percentage' => '27.34',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'AA0002G05810' => array(
		'gene_id' => 'AA0002G05810',
		'e_value' => '2e-15',
		'bit_score' => '80.5',
		'alignment_length' => '60',
		'identity_percentage' => '58.33',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'ES0263G00050' => array(
		'gene_id' => 'ES0263G00050',
		'e_value' => '2e-15',
		'bit_score' => '75.9',
		'alignment_length' => '91',
		'identity_percentage' => '42.86',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P012544'
		)
	),
	'PI00G65760' => array(
		'gene_id' => 'PI00G65760',
		'e_value' => '2e-15',
		'bit_score' => '79.7',
		'alignment_length' => '269',
		'identity_percentage' => '26.39',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P130752'
		)
	),
	'OT_17G01960' => array(
		'gene_id' => 'OT_17G01960',
		'e_value' => '7e-15',
		'bit_score' => '79.0',
		'alignment_length' => '218',
		'identity_percentage' => '27.06',
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'gf' => array(
			'HOMFAM' => 'HOM03P012932',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'emh349180' => array(
		'gene_id' => 'emh349180',
		'e_value' => '8e-15',
		'bit_score' => '76.6',
		'alignment_length' => '196',
		'identity_percentage' => '30.61',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P113167'
		)
	),
	'CR03G07040' => array(
		'gene_id' => 'CR03G07040',
		'e_value' => '2e-13',
		'bit_score' => '75.1',
		'alignment_length' => '272',
		'identity_percentage' => '28.68',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P006431'
		)
	),
	'MRCC299_05G06940' => array(
		'gene_id' => 'MRCC299_05G06940',
		'e_value' => '1e-12',
		'bit_score' => '72.8',
		'alignment_length' => '252',
		'identity_percentage' => '29.76',
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'gf' => array(
			'HOMFAM' => 'HOM03P012932',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'CR03G06520' => array(
		'gene_id' => 'CR03G06520',
		'e_value' => '1e-12',
		'bit_score' => '72.0',
		'alignment_length' => '180',
		'identity_percentage' => '29.44',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P033528'
		)
	),
	'OL16G02020' => array(
		'gene_id' => 'OL16G02020',
		'e_value' => '1e-09',
		'bit_score' => '62.8',
		'alignment_length' => '219',
		'identity_percentage' => '25.57',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P012932',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'ORCC809_16G00660' => array(
		'gene_id' => 'ORCC809_16G00660',
		'e_value' => '2e-09',
		'bit_score' => '62.4',
		'alignment_length' => '221',
		'identity_percentage' => '24.89',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P012932',
			'ORTHOFAM' => 'ORTHO03P012832'
		)
	),
	'FBgn0040321' => array(
		'gene_id' => 'FBgn0040321',
		'e_value' => '3e-08',
		'bit_score' => '58.9',
		'alignment_length' => '286',
		'identity_percentage' => '25.87',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P012272',
			'ORTHOFAM' => 'ORTHO03P022962'
		)
	),
	'ES0059G00670' => array(
		'gene_id' => 'ES0059G00670',
		'e_value' => '4e-08',
		'bit_score' => '54.7',
		'alignment_length' => '75',
		'identity_percentage' => '40.00',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P135554'
		)
	),
	'emh26090' => array(
		'gene_id' => 'emh26090',
		'e_value' => '6e-07',
		'bit_score' => '52.0',
		'alignment_length' => '111',
		'identity_percentage' => '33.33',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P001374',
			'ORTHOFAM' => 'ORTHO03P109773'
		)
	),
	'emh55400' => array(
		'gene_id' => 'emh55400',
		'e_value' => '3e-06',
		'bit_score' => '52.4',
		'alignment_length' => '226',
		'identity_percentage' => '24.78',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P015309',
			'ORTHOFAM' => 'ORTHO03P034004'
		)
	)
)
$similarity_hits_species = array(
	'esi' => array(
		(int) 0 => 'ES0121G00230',
		(int) 1 => 'ES0121G00040',
		(int) 2 => 'ES0059G00510',
		(int) 3 => 'ES0263G00050',
		(int) 4 => 'ES0059G00670'
	),
	'tps' => array(
		(int) 0 => 'TP07G01900'
	),
	'ptri' => array(
		(int) 0 => 'PTI_12G00880',
		(int) 1 => 'PTI_20G01150'
	),
	'aan' => array(
		(int) 0 => 'AA0012G00100',
		(int) 1 => 'AA0011G02170',
		(int) 2 => 'AA0002G06930',
		(int) 3 => 'AA0017G01560',
		(int) 4 => 'AA0007G00910',
		(int) 5 => 'AA0002G05820',
		(int) 6 => 'AA0002G05810'
	),
	'cvu' => array(
		(int) 0 => 'CV00G91850'
	),
	'cnc64a' => array(
		(int) 0 => 'CNC64A_001G03160',
		(int) 1 => 'CNC64A_005G01530',
		(int) 2 => 'CNC64A_009G00520',
		(int) 3 => 'CNC64A_019G01080',
		(int) 4 => 'CNC64A_025G00190'
	),
	'hsp' => array(
		(int) 0 => 'HE0000G06670'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.01g01950',
		(int) 1 => 'RCC4223.07g03960',
		(int) 2 => 'RCC4223.03g08350',
		(int) 3 => 'RCC4223.02g06100',
		(int) 4 => 'RCC4223.03g07040',
		(int) 5 => 'RCC4223.01g05230',
		(int) 6 => 'RCC4223.07g03950'
	),
	'pse3' => array(
		(int) 0 => 'PI00G42800',
		(int) 1 => 'PI00G33460',
		(int) 2 => 'PI00G15880',
		(int) 3 => 'PI00G29440',
		(int) 4 => 'PI00G30540',
		(int) 5 => 'PI00G47900',
		(int) 6 => 'PI00G03960',
		(int) 7 => 'PI00G42810',
		(int) 8 => 'PI00G65760'
	),
	'vca' => array(
		(int) 0 => 'VC00G18900',
		(int) 1 => 'VC00G18880'
	),
	'apr' => array(
		(int) 0 => 'AP00G23920'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0280263'
	),
	'emh' => array(
		(int) 0 => 'emh173790',
		(int) 1 => 'emh664230',
		(int) 2 => 'emh466680',
		(int) 3 => 'emh62480',
		(int) 4 => 'emh572420',
		(int) 5 => 'emh349180',
		(int) 6 => 'emh26090',
		(int) 7 => 'emh55400'
	),
	'nga' => array(
		(int) 0 => 'Naga_100043g13'
	),
	'cre' => array(
		(int) 0 => 'CR02G10720',
		(int) 1 => 'CR03G07040',
		(int) 2 => 'CR03G06520'
	),
	'ota' => array(
		(int) 0 => 'OT_17G01960'
	),
	'mrcc299' => array(
		(int) 0 => 'MRCC299_05G06940'
	),
	'olu' => array(
		(int) 0 => 'OL16G02020'
	),
	'orcc809' => array(
		(int) 0 => 'ORCC809_16G00660'
	),
	'drm' => array(
		(int) 0 => 'FBgn0040321'
	)
)
$gene_id = 'ES0121G00230'
$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 = 'ES0121G00230'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'AT2G20410'
$gf_placeholder = 'HOM03P030720'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_081G00020',
	'e_value' => '5e-18',
	'bit_score' => '85.1',
	'alignment_length' => '200',
	'identity_percentage' => '31.00',
	'gf' => array(
		'HOMFAM' => 'HOM03P001374',
		'ORTHOFAM' => 'ORTHO03P047980'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_081G00020'
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