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(
		'FC003G09000' => array(
			'gene_id' => 'FC003G09000',
			'e_value' => '0.0',
			'bit_score' => '3596',
			'alignment_length' => '1738',
			'identity_percentage' => '100.00',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_21G02570' => array(
			'gene_id' => 'PTI_21G02570',
			'e_value' => '0.0',
			'bit_score' => '1242',
			'alignment_length' => '1746',
			'identity_percentage' => '41.41',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100001g67' => array(
			'gene_id' => 'Naga_100001g67',
			'e_value' => '4e-81',
			'bit_score' => '301',
			'alignment_length' => '1353',
			'identity_percentage' => '24.32',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'phs344240' => array(
			'gene_id' => 'phs344240',
			'e_value' => '4e-64',
			'bit_score' => '243',
			'alignment_length' => '1106',
			'identity_percentage' => '25.50',
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00270G00460' => array(
			'gene_id' => 'PP00270G00460',
			'e_value' => '3e-40',
			'bit_score' => '167',
			'alignment_length' => '483',
			'identity_percentage' => '29.19',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G57300' => array(
			'gene_id' => 'OS03G57300',
			'e_value' => '3e-38',
			'bit_score' => '161',
			'alignment_length' => '480',
			'identity_percentage' => '30.00',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT5G16280' => array(
			'gene_id' => 'AT5G16280',
			'e_value' => '5e-36',
			'bit_score' => '154',
			'alignment_length' => '536',
			'identity_percentage' => '25.93',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00030G00120' => array(
			'gene_id' => 'ATR_00030G00120',
			'e_value' => '4e-34',
			'bit_score' => '147',
			'alignment_length' => '523',
			'identity_percentage' => '27.92',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G05540' => array(
			'gene_id' => 'CV00G05540',
			'e_value' => '3e-28',
			'bit_score' => '128',
			'alignment_length' => '637',
			'identity_percentage' => '24.33',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MRCC299_03G08000' => array(
			'gene_id' => 'MRCC299_03G08000',
			'e_value' => '2e-27',
			'bit_score' => '125',
			'alignment_length' => '476',
			'identity_percentage' => '27.73',
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0024G00080' => array(
			'gene_id' => 'AA0024G00080',
			'e_value' => '3e-27',
			'bit_score' => '125',
			'alignment_length' => '684',
			'identity_percentage' => '26.02',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G45200' => array(
			'gene_id' => 'AC00G45200',
			'e_value' => '4e-26',
			'bit_score' => '121',
			'alignment_length' => '603',
			'identity_percentage' => '24.88',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0026G00250' => array(
			'gene_id' => 'AA0026G00250',
			'e_value' => '1e-24',
			'bit_score' => '117',
			'alignment_length' => '535',
			'identity_percentage' => '27.66',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000153339' => array(
			'gene_id' => 'ENSG00000153339',
			'e_value' => '1e-24',
			'bit_score' => '116',
			'alignment_length' => '481',
			'identity_percentage' => '22.66',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000033382' => array(
			'gene_id' => 'ENSMUSG00000033382',
			'e_value' => '2e-24',
			'bit_score' => '116',
			'alignment_length' => '481',
			'identity_percentage' => '24.12',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0205G00170' => array(
			'gene_id' => 'ES0205G00170',
			'e_value' => '5e-24',
			'bit_score' => '111',
			'alignment_length' => '449',
			'identity_percentage' => '26.28',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0260655' => array(
			'gene_id' => 'FBgn0260655',
			'e_value' => '8e-24',
			'bit_score' => '114',
			'alignment_length' => '393',
			'identity_percentage' => '24.94',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL17G01190' => array(
			'gene_id' => 'OL17G01190',
			'e_value' => '5e-22',
			'bit_score' => '108',
			'alignment_length' => '443',
			'identity_percentage' => '25.06',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR01G05390' => array(
			'gene_id' => 'CR01G05390',
			'e_value' => '6e-22',
			'bit_score' => '108',
			'alignment_length' => '677',
			'identity_percentage' => '22.45',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OM_18G01010' => array(
			'gene_id' => 'OM_18G01010',
			'e_value' => '2e-20',
			'bit_score' => '103',
			'alignment_length' => '326',
			'identity_percentage' => '25.15',
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0292682' => array(
			'gene_id' => 'DDB_G0292682',
			'e_value' => '6e-20',
			'bit_score' => '101',
			'alignment_length' => '526',
			'identity_percentage' => '21.48',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OT_18G01170' => array(
			'gene_id' => 'OT_18G01170',
			'e_value' => '7e-20',
			'bit_score' => '101',
			'alignment_length' => '405',
			'identity_percentage' => '24.20',
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ORCC809_17G01190' => array(
			'gene_id' => 'ORCC809_17G01190',
			'e_value' => '6e-19',
			'bit_score' => '98.2',
			'alignment_length' => '472',
			'identity_percentage' => '24.36',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0205G00050' => array(
			'gene_id' => 'ES0205G00050',
			'e_value' => '3e-18',
			'bit_score' => '96.3',
			'alignment_length' => '633',
			'identity_percentage' => '23.22',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G45660' => array(
			'gene_id' => 'VC00G45660',
			'e_value' => '9e-18',
			'bit_score' => '94.7',
			'alignment_length' => '645',
			'identity_percentage' => '23.10',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_003G00260' => array(
			'gene_id' => 'CNC64A_003G00260',
			'e_value' => '1e-14',
			'bit_score' => '83.6',
			'alignment_length' => '425',
			'identity_percentage' => '25.65',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_003G00300' => array(
			'gene_id' => 'CNC64A_003G00300',
			'e_value' => '1e-14',
			'bit_score' => '83.6',
			'alignment_length' => '425',
			'identity_percentage' => '25.65',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MP17G02120' => array(
			'gene_id' => 'MP17G02120',
			'e_value' => '2e-13',
			'bit_score' => '80.5',
			'alignment_length' => '334',
			'identity_percentage' => '26.05',
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G14610' => array(
			'gene_id' => 'PI00G14610',
			'e_value' => '2e-12',
			'bit_score' => '76.6',
			'alignment_length' => '316',
			'identity_percentage' => '23.42',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00018512' => array(
			'gene_id' => 'WBGene00018512',
			'e_value' => '2e-11',
			'bit_score' => '73.9',
			'alignment_length' => '231',
			'identity_percentage' => '28.14',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_094G00020' => array(
			'gene_id' => 'CNC64A_094G00020',
			'e_value' => '4e-11',
			'bit_score' => '69.7',
			'alignment_length' => '250',
			'identity_percentage' => '28.00',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.05g02320' => array(
			'gene_id' => 'RCC4223.05g02320',
			'e_value' => '3e-10',
			'bit_score' => '69.7',
			'alignment_length' => '363',
			'identity_percentage' => '21.49',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'BPRRCC1105_09G00820' => array(
			'gene_id' => 'BPRRCC1105_09G00820',
			'e_value' => '1e-07',
			'bit_score' => '61.2',
			'alignment_length' => '338',
			'identity_percentage' => '24.85',
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G64240' => array(
			'gene_id' => 'AP00G64240',
			'e_value' => '5e-07',
			'bit_score' => '58.9',
			'alignment_length' => '120',
			'identity_percentage' => '28.33',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'fcy' => array(
			(int) 0 => 'FC003G09000'
		),
		'ptri' => array(
			(int) 0 => 'PTI_21G02570'
		),
		'nga' => array(
			(int) 0 => 'Naga_100001g67'
		),
		'phs' => array(
			(int) 0 => 'phs344240'
		),
		'ppa' => array(
			(int) 0 => 'PP00270G00460'
		),
		'osa' => array(
			(int) 0 => 'OS03G57300'
		),
		'ath' => array(
			(int) 0 => 'AT5G16280'
		),
		'atr' => array(
			(int) 0 => 'ATR_00030G00120'
		),
		'cvu' => array(
			(int) 0 => 'CV00G05540'
		),
		'mrcc299' => array(
			(int) 0 => 'MRCC299_03G08000'
		),
		'aan' => array(
			(int) 0 => 'AA0024G00080',
			(int) 1 => 'AA0026G00250'
		),
		'acg' => array(
			(int) 0 => 'AC00G45200'
		),
		'hom' => array(
			(int) 0 => 'ENSG00000153339'
		),
		'mus' => array(
			(int) 0 => 'ENSMUSG00000033382'
		),
		'esi' => array(
			(int) 0 => 'ES0205G00170',
			(int) 1 => 'ES0205G00050'
		),
		'drm' => array(
			(int) 0 => 'FBgn0260655'
		),
		'olu' => array(
			(int) 0 => 'OL17G01190'
		),
		'cre' => array(
			(int) 0 => 'CR01G05390'
		),
		'ome' => array(
			(int) 0 => 'OM_18G01010'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0292682'
		),
		'ota' => array(
			(int) 0 => 'OT_18G01170'
		),
		'orcc809' => array(
			(int) 0 => 'ORCC809_17G01190'
		),
		'vca' => array(
			(int) 0 => 'VC00G45660'
		),
		'cnc64a' => array(
			(int) 0 => 'CNC64A_003G00260',
			(int) 1 => 'CNC64A_003G00300'
		),
		'mpu' => array(
			(int) 0 => 'MP17G02120'
		),
		'pse3' => array(
			(int) 0 => 'PI00G14610'
		),
		'cel' => array(
			(int) 0 => 'WBGene00018512'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.05g02320'
		),
		'bprrcc1105' => array(
			(int) 0 => 'BPRRCC1105_09G00820'
		),
		'apr' => array(
			(int) 0 => 'AP00G64240'
		)
	),
	'gene_id' => 'FC003G09000',
	'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' => 'FC003G09000',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'MP01G04550',
	'gf_placeholder' => 'HOM03P020323',
	'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(
	'FC003G09000' => array(
		'gene_id' => 'FC003G09000',
		'e_value' => '0.0',
		'bit_score' => '3596',
		'alignment_length' => '1738',
		'identity_percentage' => '100.00',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P038607'
		)
	),
	'PTI_21G02570' => array(
		'gene_id' => 'PTI_21G02570',
		'e_value' => '0.0',
		'bit_score' => '1242',
		'alignment_length' => '1746',
		'identity_percentage' => '41.41',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P038607'
		)
	),
	'Naga_100001g67' => array(
		'gene_id' => 'Naga_100001g67',
		'e_value' => '4e-81',
		'bit_score' => '301',
		'alignment_length' => '1353',
		'identity_percentage' => '24.32',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P038607'
		)
	),
	'phs344240' => array(
		'gene_id' => 'phs344240',
		'e_value' => '4e-64',
		'bit_score' => '243',
		'alignment_length' => '1106',
		'identity_percentage' => '25.50',
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'PP00270G00460' => array(
		'gene_id' => 'PP00270G00460',
		'e_value' => '3e-40',
		'bit_score' => '167',
		'alignment_length' => '483',
		'identity_percentage' => '29.19',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'OS03G57300' => array(
		'gene_id' => 'OS03G57300',
		'e_value' => '3e-38',
		'bit_score' => '161',
		'alignment_length' => '480',
		'identity_percentage' => '30.00',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'AT5G16280' => array(
		'gene_id' => 'AT5G16280',
		'e_value' => '5e-36',
		'bit_score' => '154',
		'alignment_length' => '536',
		'identity_percentage' => '25.93',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ATR_00030G00120' => array(
		'gene_id' => 'ATR_00030G00120',
		'e_value' => '4e-34',
		'bit_score' => '147',
		'alignment_length' => '523',
		'identity_percentage' => '27.92',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CV00G05540' => array(
		'gene_id' => 'CV00G05540',
		'e_value' => '3e-28',
		'bit_score' => '128',
		'alignment_length' => '637',
		'identity_percentage' => '24.33',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'MRCC299_03G08000' => array(
		'gene_id' => 'MRCC299_03G08000',
		'e_value' => '2e-27',
		'bit_score' => '125',
		'alignment_length' => '476',
		'identity_percentage' => '27.73',
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'AA0024G00080' => array(
		'gene_id' => 'AA0024G00080',
		'e_value' => '3e-27',
		'bit_score' => '125',
		'alignment_length' => '684',
		'identity_percentage' => '26.02',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P034960',
			'ORTHOFAM' => 'ORTHO03P034674'
		)
	),
	'AC00G45200' => array(
		'gene_id' => 'AC00G45200',
		'e_value' => '4e-26',
		'bit_score' => '121',
		'alignment_length' => '603',
		'identity_percentage' => '24.88',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'AA0026G00250' => array(
		'gene_id' => 'AA0026G00250',
		'e_value' => '1e-24',
		'bit_score' => '117',
		'alignment_length' => '535',
		'identity_percentage' => '27.66',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P034960',
			'ORTHOFAM' => 'ORTHO03P034674'
		)
	),
	'ENSG00000153339' => array(
		'gene_id' => 'ENSG00000153339',
		'e_value' => '1e-24',
		'bit_score' => '116',
		'alignment_length' => '481',
		'identity_percentage' => '22.66',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ENSMUSG00000033382' => array(
		'gene_id' => 'ENSMUSG00000033382',
		'e_value' => '2e-24',
		'bit_score' => '116',
		'alignment_length' => '481',
		'identity_percentage' => '24.12',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ES0205G00170' => array(
		'gene_id' => 'ES0205G00170',
		'e_value' => '5e-24',
		'bit_score' => '111',
		'alignment_length' => '449',
		'identity_percentage' => '26.28',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P034674'
		)
	),
	'FBgn0260655' => array(
		'gene_id' => 'FBgn0260655',
		'e_value' => '8e-24',
		'bit_score' => '114',
		'alignment_length' => '393',
		'identity_percentage' => '24.94',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'OL17G01190' => array(
		'gene_id' => 'OL17G01190',
		'e_value' => '5e-22',
		'bit_score' => '108',
		'alignment_length' => '443',
		'identity_percentage' => '25.06',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CR01G05390' => array(
		'gene_id' => 'CR01G05390',
		'e_value' => '6e-22',
		'bit_score' => '108',
		'alignment_length' => '677',
		'identity_percentage' => '22.45',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'OM_18G01010' => array(
		'gene_id' => 'OM_18G01010',
		'e_value' => '2e-20',
		'bit_score' => '103',
		'alignment_length' => '326',
		'identity_percentage' => '25.15',
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'DDB_G0292682' => array(
		'gene_id' => 'DDB_G0292682',
		'e_value' => '6e-20',
		'bit_score' => '101',
		'alignment_length' => '526',
		'identity_percentage' => '21.48',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'OT_18G01170' => array(
		'gene_id' => 'OT_18G01170',
		'e_value' => '7e-20',
		'bit_score' => '101',
		'alignment_length' => '405',
		'identity_percentage' => '24.20',
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ORCC809_17G01190' => array(
		'gene_id' => 'ORCC809_17G01190',
		'e_value' => '6e-19',
		'bit_score' => '98.2',
		'alignment_length' => '472',
		'identity_percentage' => '24.36',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ES0205G00050' => array(
		'gene_id' => 'ES0205G00050',
		'e_value' => '3e-18',
		'bit_score' => '96.3',
		'alignment_length' => '633',
		'identity_percentage' => '23.22',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P201126'
		)
	),
	'VC00G45660' => array(
		'gene_id' => 'VC00G45660',
		'e_value' => '9e-18',
		'bit_score' => '94.7',
		'alignment_length' => '645',
		'identity_percentage' => '23.10',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CNC64A_003G00260' => array(
		'gene_id' => 'CNC64A_003G00260',
		'e_value' => '1e-14',
		'bit_score' => '83.6',
		'alignment_length' => '425',
		'identity_percentage' => '25.65',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CNC64A_003G00300' => array(
		'gene_id' => 'CNC64A_003G00300',
		'e_value' => '1e-14',
		'bit_score' => '83.6',
		'alignment_length' => '425',
		'identity_percentage' => '25.65',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'MP17G02120' => array(
		'gene_id' => 'MP17G02120',
		'e_value' => '2e-13',
		'bit_score' => '80.5',
		'alignment_length' => '334',
		'identity_percentage' => '26.05',
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'PI00G14610' => array(
		'gene_id' => 'PI00G14610',
		'e_value' => '2e-12',
		'bit_score' => '76.6',
		'alignment_length' => '316',
		'identity_percentage' => '23.42',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'WBGene00018512' => array(
		'gene_id' => 'WBGene00018512',
		'e_value' => '2e-11',
		'bit_score' => '73.9',
		'alignment_length' => '231',
		'identity_percentage' => '28.14',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CNC64A_094G00020' => array(
		'gene_id' => 'CNC64A_094G00020',
		'e_value' => '4e-11',
		'bit_score' => '69.7',
		'alignment_length' => '250',
		'identity_percentage' => '28.00',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'RCC4223.05g02320' => array(
		'gene_id' => 'RCC4223.05g02320',
		'e_value' => '3e-10',
		'bit_score' => '69.7',
		'alignment_length' => '363',
		'identity_percentage' => '21.49',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'BPRRCC1105_09G00820' => array(
		'gene_id' => 'BPRRCC1105_09G00820',
		'e_value' => '1e-07',
		'bit_score' => '61.2',
		'alignment_length' => '338',
		'identity_percentage' => '24.85',
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'AP00G64240' => array(
		'gene_id' => 'AP00G64240',
		'e_value' => '5e-07',
		'bit_score' => '58.9',
		'alignment_length' => '120',
		'identity_percentage' => '28.33',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	)
)
$similarity_hits_species = array(
	'fcy' => array(
		(int) 0 => 'FC003G09000'
	),
	'ptri' => array(
		(int) 0 => 'PTI_21G02570'
	),
	'nga' => array(
		(int) 0 => 'Naga_100001g67'
	),
	'phs' => array(
		(int) 0 => 'phs344240'
	),
	'ppa' => array(
		(int) 0 => 'PP00270G00460'
	),
	'osa' => array(
		(int) 0 => 'OS03G57300'
	),
	'ath' => array(
		(int) 0 => 'AT5G16280'
	),
	'atr' => array(
		(int) 0 => 'ATR_00030G00120'
	),
	'cvu' => array(
		(int) 0 => 'CV00G05540'
	),
	'mrcc299' => array(
		(int) 0 => 'MRCC299_03G08000'
	),
	'aan' => array(
		(int) 0 => 'AA0024G00080',
		(int) 1 => 'AA0026G00250'
	),
	'acg' => array(
		(int) 0 => 'AC00G45200'
	),
	'hom' => array(
		(int) 0 => 'ENSG00000153339'
	),
	'mus' => array(
		(int) 0 => 'ENSMUSG00000033382'
	),
	'esi' => array(
		(int) 0 => 'ES0205G00170',
		(int) 1 => 'ES0205G00050'
	),
	'drm' => array(
		(int) 0 => 'FBgn0260655'
	),
	'olu' => array(
		(int) 0 => 'OL17G01190'
	),
	'cre' => array(
		(int) 0 => 'CR01G05390'
	),
	'ome' => array(
		(int) 0 => 'OM_18G01010'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0292682'
	),
	'ota' => array(
		(int) 0 => 'OT_18G01170'
	),
	'orcc809' => array(
		(int) 0 => 'ORCC809_17G01190'
	),
	'vca' => array(
		(int) 0 => 'VC00G45660'
	),
	'cnc64a' => array(
		(int) 0 => 'CNC64A_003G00260',
		(int) 1 => 'CNC64A_003G00300'
	),
	'mpu' => array(
		(int) 0 => 'MP17G02120'
	),
	'pse3' => array(
		(int) 0 => 'PI00G14610'
	),
	'cel' => array(
		(int) 0 => 'WBGene00018512'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.05g02320'
	),
	'bprrcc1105' => array(
		(int) 0 => 'BPRRCC1105_09G00820'
	),
	'apr' => array(
		(int) 0 => 'AP00G64240'
	)
)
$gene_id = 'FC003G09000'
$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 = 'FC003G09000'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'MP01G04550'
$gf_placeholder = 'HOM03P020323'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_094G00020',
	'e_value' => '4e-11',
	'bit_score' => '69.7',
	'alignment_length' => '250',
	'identity_percentage' => '28.00',
	'gf' => array(
		'HOMFAM' => 'HOM03P002585',
		'ORTHOFAM' => 'ORTHO03P002556'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_094G00020'
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(
		'FC003G09000' => array(
			'gene_id' => 'FC003G09000',
			'e_value' => '0.0',
			'bit_score' => '3596',
			'alignment_length' => '1738',
			'identity_percentage' => '100.00',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_21G02570' => array(
			'gene_id' => 'PTI_21G02570',
			'e_value' => '0.0',
			'bit_score' => '1242',
			'alignment_length' => '1746',
			'identity_percentage' => '41.41',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100001g67' => array(
			'gene_id' => 'Naga_100001g67',
			'e_value' => '4e-81',
			'bit_score' => '301',
			'alignment_length' => '1353',
			'identity_percentage' => '24.32',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'phs344240' => array(
			'gene_id' => 'phs344240',
			'e_value' => '4e-64',
			'bit_score' => '243',
			'alignment_length' => '1106',
			'identity_percentage' => '25.50',
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00270G00460' => array(
			'gene_id' => 'PP00270G00460',
			'e_value' => '3e-40',
			'bit_score' => '167',
			'alignment_length' => '483',
			'identity_percentage' => '29.19',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G57300' => array(
			'gene_id' => 'OS03G57300',
			'e_value' => '3e-38',
			'bit_score' => '161',
			'alignment_length' => '480',
			'identity_percentage' => '30.00',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT5G16280' => array(
			'gene_id' => 'AT5G16280',
			'e_value' => '5e-36',
			'bit_score' => '154',
			'alignment_length' => '536',
			'identity_percentage' => '25.93',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00030G00120' => array(
			'gene_id' => 'ATR_00030G00120',
			'e_value' => '4e-34',
			'bit_score' => '147',
			'alignment_length' => '523',
			'identity_percentage' => '27.92',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G05540' => array(
			'gene_id' => 'CV00G05540',
			'e_value' => '3e-28',
			'bit_score' => '128',
			'alignment_length' => '637',
			'identity_percentage' => '24.33',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MRCC299_03G08000' => array(
			'gene_id' => 'MRCC299_03G08000',
			'e_value' => '2e-27',
			'bit_score' => '125',
			'alignment_length' => '476',
			'identity_percentage' => '27.73',
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0024G00080' => array(
			'gene_id' => 'AA0024G00080',
			'e_value' => '3e-27',
			'bit_score' => '125',
			'alignment_length' => '684',
			'identity_percentage' => '26.02',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G45200' => array(
			'gene_id' => 'AC00G45200',
			'e_value' => '4e-26',
			'bit_score' => '121',
			'alignment_length' => '603',
			'identity_percentage' => '24.88',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0026G00250' => array(
			'gene_id' => 'AA0026G00250',
			'e_value' => '1e-24',
			'bit_score' => '117',
			'alignment_length' => '535',
			'identity_percentage' => '27.66',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000153339' => array(
			'gene_id' => 'ENSG00000153339',
			'e_value' => '1e-24',
			'bit_score' => '116',
			'alignment_length' => '481',
			'identity_percentage' => '22.66',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000033382' => array(
			'gene_id' => 'ENSMUSG00000033382',
			'e_value' => '2e-24',
			'bit_score' => '116',
			'alignment_length' => '481',
			'identity_percentage' => '24.12',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0205G00170' => array(
			'gene_id' => 'ES0205G00170',
			'e_value' => '5e-24',
			'bit_score' => '111',
			'alignment_length' => '449',
			'identity_percentage' => '26.28',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0260655' => array(
			'gene_id' => 'FBgn0260655',
			'e_value' => '8e-24',
			'bit_score' => '114',
			'alignment_length' => '393',
			'identity_percentage' => '24.94',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL17G01190' => array(
			'gene_id' => 'OL17G01190',
			'e_value' => '5e-22',
			'bit_score' => '108',
			'alignment_length' => '443',
			'identity_percentage' => '25.06',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR01G05390' => array(
			'gene_id' => 'CR01G05390',
			'e_value' => '6e-22',
			'bit_score' => '108',
			'alignment_length' => '677',
			'identity_percentage' => '22.45',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OM_18G01010' => array(
			'gene_id' => 'OM_18G01010',
			'e_value' => '2e-20',
			'bit_score' => '103',
			'alignment_length' => '326',
			'identity_percentage' => '25.15',
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0292682' => array(
			'gene_id' => 'DDB_G0292682',
			'e_value' => '6e-20',
			'bit_score' => '101',
			'alignment_length' => '526',
			'identity_percentage' => '21.48',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OT_18G01170' => array(
			'gene_id' => 'OT_18G01170',
			'e_value' => '7e-20',
			'bit_score' => '101',
			'alignment_length' => '405',
			'identity_percentage' => '24.20',
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ORCC809_17G01190' => array(
			'gene_id' => 'ORCC809_17G01190',
			'e_value' => '6e-19',
			'bit_score' => '98.2',
			'alignment_length' => '472',
			'identity_percentage' => '24.36',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0205G00050' => array(
			'gene_id' => 'ES0205G00050',
			'e_value' => '3e-18',
			'bit_score' => '96.3',
			'alignment_length' => '633',
			'identity_percentage' => '23.22',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G45660' => array(
			'gene_id' => 'VC00G45660',
			'e_value' => '9e-18',
			'bit_score' => '94.7',
			'alignment_length' => '645',
			'identity_percentage' => '23.10',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_003G00260' => array(
			'gene_id' => 'CNC64A_003G00260',
			'e_value' => '1e-14',
			'bit_score' => '83.6',
			'alignment_length' => '425',
			'identity_percentage' => '25.65',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_003G00300' => array(
			'gene_id' => 'CNC64A_003G00300',
			'e_value' => '1e-14',
			'bit_score' => '83.6',
			'alignment_length' => '425',
			'identity_percentage' => '25.65',
			'species' => 'cnc64a',
			'common_name' => 'Chlorella sp NC64A',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MP17G02120' => array(
			'gene_id' => 'MP17G02120',
			'e_value' => '2e-13',
			'bit_score' => '80.5',
			'alignment_length' => '334',
			'identity_percentage' => '26.05',
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G14610' => array(
			'gene_id' => 'PI00G14610',
			'e_value' => '2e-12',
			'bit_score' => '76.6',
			'alignment_length' => '316',
			'identity_percentage' => '23.42',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00018512' => array(
			'gene_id' => 'WBGene00018512',
			'e_value' => '2e-11',
			'bit_score' => '73.9',
			'alignment_length' => '231',
			'identity_percentage' => '28.14',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_094G00020' => array(
			'gene_id' => 'CNC64A_094G00020',
			'e_value' => '4e-11',
			'bit_score' => '69.7',
			'alignment_length' => '250',
			'identity_percentage' => '28.00',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.05g02320' => array(
			'gene_id' => 'RCC4223.05g02320',
			'e_value' => '3e-10',
			'bit_score' => '69.7',
			'alignment_length' => '363',
			'identity_percentage' => '21.49',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'BPRRCC1105_09G00820' => array(
			'gene_id' => 'BPRRCC1105_09G00820',
			'e_value' => '1e-07',
			'bit_score' => '61.2',
			'alignment_length' => '338',
			'identity_percentage' => '24.85',
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G64240' => array(
			'gene_id' => 'AP00G64240',
			'e_value' => '5e-07',
			'bit_score' => '58.9',
			'alignment_length' => '120',
			'identity_percentage' => '28.33',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'fcy' => array(
			(int) 0 => 'FC003G09000'
		),
		'ptri' => array(
			(int) 0 => 'PTI_21G02570'
		),
		'nga' => array(
			(int) 0 => 'Naga_100001g67'
		),
		'phs' => array(
			(int) 0 => 'phs344240'
		),
		'ppa' => array(
			(int) 0 => 'PP00270G00460'
		),
		'osa' => array(
			(int) 0 => 'OS03G57300'
		),
		'ath' => array(
			(int) 0 => 'AT5G16280'
		),
		'atr' => array(
			(int) 0 => 'ATR_00030G00120'
		),
		'cvu' => array(
			(int) 0 => 'CV00G05540'
		),
		'mrcc299' => array(
			(int) 0 => 'MRCC299_03G08000'
		),
		'aan' => array(
			(int) 0 => 'AA0024G00080',
			(int) 1 => 'AA0026G00250'
		),
		'acg' => array(
			(int) 0 => 'AC00G45200'
		),
		'hom' => array(
			(int) 0 => 'ENSG00000153339'
		),
		'mus' => array(
			(int) 0 => 'ENSMUSG00000033382'
		),
		'esi' => array(
			(int) 0 => 'ES0205G00170',
			(int) 1 => 'ES0205G00050'
		),
		'drm' => array(
			(int) 0 => 'FBgn0260655'
		),
		'olu' => array(
			(int) 0 => 'OL17G01190'
		),
		'cre' => array(
			(int) 0 => 'CR01G05390'
		),
		'ome' => array(
			(int) 0 => 'OM_18G01010'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0292682'
		),
		'ota' => array(
			(int) 0 => 'OT_18G01170'
		),
		'orcc809' => array(
			(int) 0 => 'ORCC809_17G01190'
		),
		'vca' => array(
			(int) 0 => 'VC00G45660'
		),
		'cnc64a' => array(
			(int) 0 => 'CNC64A_003G00260',
			(int) 1 => 'CNC64A_003G00300'
		),
		'mpu' => array(
			(int) 0 => 'MP17G02120'
		),
		'pse3' => array(
			(int) 0 => 'PI00G14610'
		),
		'cel' => array(
			(int) 0 => 'WBGene00018512'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.05g02320'
		),
		'bprrcc1105' => array(
			(int) 0 => 'BPRRCC1105_09G00820'
		),
		'apr' => array(
			(int) 0 => 'AP00G64240'
		)
	),
	'gene_id' => 'FC003G09000',
	'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' => 'FC003G09000',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'MP01G04550',
	'gf_placeholder' => 'HOM03P020323',
	'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(
	'FC003G09000' => array(
		'gene_id' => 'FC003G09000',
		'e_value' => '0.0',
		'bit_score' => '3596',
		'alignment_length' => '1738',
		'identity_percentage' => '100.00',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P038607'
		)
	),
	'PTI_21G02570' => array(
		'gene_id' => 'PTI_21G02570',
		'e_value' => '0.0',
		'bit_score' => '1242',
		'alignment_length' => '1746',
		'identity_percentage' => '41.41',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P038607'
		)
	),
	'Naga_100001g67' => array(
		'gene_id' => 'Naga_100001g67',
		'e_value' => '4e-81',
		'bit_score' => '301',
		'alignment_length' => '1353',
		'identity_percentage' => '24.32',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P038607'
		)
	),
	'phs344240' => array(
		'gene_id' => 'phs344240',
		'e_value' => '4e-64',
		'bit_score' => '243',
		'alignment_length' => '1106',
		'identity_percentage' => '25.50',
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'PP00270G00460' => array(
		'gene_id' => 'PP00270G00460',
		'e_value' => '3e-40',
		'bit_score' => '167',
		'alignment_length' => '483',
		'identity_percentage' => '29.19',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'OS03G57300' => array(
		'gene_id' => 'OS03G57300',
		'e_value' => '3e-38',
		'bit_score' => '161',
		'alignment_length' => '480',
		'identity_percentage' => '30.00',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'AT5G16280' => array(
		'gene_id' => 'AT5G16280',
		'e_value' => '5e-36',
		'bit_score' => '154',
		'alignment_length' => '536',
		'identity_percentage' => '25.93',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ATR_00030G00120' => array(
		'gene_id' => 'ATR_00030G00120',
		'e_value' => '4e-34',
		'bit_score' => '147',
		'alignment_length' => '523',
		'identity_percentage' => '27.92',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CV00G05540' => array(
		'gene_id' => 'CV00G05540',
		'e_value' => '3e-28',
		'bit_score' => '128',
		'alignment_length' => '637',
		'identity_percentage' => '24.33',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'MRCC299_03G08000' => array(
		'gene_id' => 'MRCC299_03G08000',
		'e_value' => '2e-27',
		'bit_score' => '125',
		'alignment_length' => '476',
		'identity_percentage' => '27.73',
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'AA0024G00080' => array(
		'gene_id' => 'AA0024G00080',
		'e_value' => '3e-27',
		'bit_score' => '125',
		'alignment_length' => '684',
		'identity_percentage' => '26.02',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P034960',
			'ORTHOFAM' => 'ORTHO03P034674'
		)
	),
	'AC00G45200' => array(
		'gene_id' => 'AC00G45200',
		'e_value' => '4e-26',
		'bit_score' => '121',
		'alignment_length' => '603',
		'identity_percentage' => '24.88',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'AA0026G00250' => array(
		'gene_id' => 'AA0026G00250',
		'e_value' => '1e-24',
		'bit_score' => '117',
		'alignment_length' => '535',
		'identity_percentage' => '27.66',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P034960',
			'ORTHOFAM' => 'ORTHO03P034674'
		)
	),
	'ENSG00000153339' => array(
		'gene_id' => 'ENSG00000153339',
		'e_value' => '1e-24',
		'bit_score' => '116',
		'alignment_length' => '481',
		'identity_percentage' => '22.66',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ENSMUSG00000033382' => array(
		'gene_id' => 'ENSMUSG00000033382',
		'e_value' => '2e-24',
		'bit_score' => '116',
		'alignment_length' => '481',
		'identity_percentage' => '24.12',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ES0205G00170' => array(
		'gene_id' => 'ES0205G00170',
		'e_value' => '5e-24',
		'bit_score' => '111',
		'alignment_length' => '449',
		'identity_percentage' => '26.28',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P034674'
		)
	),
	'FBgn0260655' => array(
		'gene_id' => 'FBgn0260655',
		'e_value' => '8e-24',
		'bit_score' => '114',
		'alignment_length' => '393',
		'identity_percentage' => '24.94',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'OL17G01190' => array(
		'gene_id' => 'OL17G01190',
		'e_value' => '5e-22',
		'bit_score' => '108',
		'alignment_length' => '443',
		'identity_percentage' => '25.06',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CR01G05390' => array(
		'gene_id' => 'CR01G05390',
		'e_value' => '6e-22',
		'bit_score' => '108',
		'alignment_length' => '677',
		'identity_percentage' => '22.45',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'OM_18G01010' => array(
		'gene_id' => 'OM_18G01010',
		'e_value' => '2e-20',
		'bit_score' => '103',
		'alignment_length' => '326',
		'identity_percentage' => '25.15',
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'DDB_G0292682' => array(
		'gene_id' => 'DDB_G0292682',
		'e_value' => '6e-20',
		'bit_score' => '101',
		'alignment_length' => '526',
		'identity_percentage' => '21.48',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'OT_18G01170' => array(
		'gene_id' => 'OT_18G01170',
		'e_value' => '7e-20',
		'bit_score' => '101',
		'alignment_length' => '405',
		'identity_percentage' => '24.20',
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ORCC809_17G01190' => array(
		'gene_id' => 'ORCC809_17G01190',
		'e_value' => '6e-19',
		'bit_score' => '98.2',
		'alignment_length' => '472',
		'identity_percentage' => '24.36',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'ES0205G00050' => array(
		'gene_id' => 'ES0205G00050',
		'e_value' => '3e-18',
		'bit_score' => '96.3',
		'alignment_length' => '633',
		'identity_percentage' => '23.22',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P201126'
		)
	),
	'VC00G45660' => array(
		'gene_id' => 'VC00G45660',
		'e_value' => '9e-18',
		'bit_score' => '94.7',
		'alignment_length' => '645',
		'identity_percentage' => '23.10',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CNC64A_003G00260' => array(
		'gene_id' => 'CNC64A_003G00260',
		'e_value' => '1e-14',
		'bit_score' => '83.6',
		'alignment_length' => '425',
		'identity_percentage' => '25.65',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CNC64A_003G00300' => array(
		'gene_id' => 'CNC64A_003G00300',
		'e_value' => '1e-14',
		'bit_score' => '83.6',
		'alignment_length' => '425',
		'identity_percentage' => '25.65',
		'species' => 'cnc64a',
		'common_name' => 'Chlorella sp NC64A',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'MP17G02120' => array(
		'gene_id' => 'MP17G02120',
		'e_value' => '2e-13',
		'bit_score' => '80.5',
		'alignment_length' => '334',
		'identity_percentage' => '26.05',
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'PI00G14610' => array(
		'gene_id' => 'PI00G14610',
		'e_value' => '2e-12',
		'bit_score' => '76.6',
		'alignment_length' => '316',
		'identity_percentage' => '23.42',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'WBGene00018512' => array(
		'gene_id' => 'WBGene00018512',
		'e_value' => '2e-11',
		'bit_score' => '73.9',
		'alignment_length' => '231',
		'identity_percentage' => '28.14',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'CNC64A_094G00020' => array(
		'gene_id' => 'CNC64A_094G00020',
		'e_value' => '4e-11',
		'bit_score' => '69.7',
		'alignment_length' => '250',
		'identity_percentage' => '28.00',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'RCC4223.05g02320' => array(
		'gene_id' => 'RCC4223.05g02320',
		'e_value' => '3e-10',
		'bit_score' => '69.7',
		'alignment_length' => '363',
		'identity_percentage' => '21.49',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'BPRRCC1105_09G00820' => array(
		'gene_id' => 'BPRRCC1105_09G00820',
		'e_value' => '1e-07',
		'bit_score' => '61.2',
		'alignment_length' => '338',
		'identity_percentage' => '24.85',
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	),
	'AP00G64240' => array(
		'gene_id' => 'AP00G64240',
		'e_value' => '5e-07',
		'bit_score' => '58.9',
		'alignment_length' => '120',
		'identity_percentage' => '28.33',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P002585',
			'ORTHOFAM' => 'ORTHO03P002556'
		)
	)
)
$similarity_hits_species = array(
	'fcy' => array(
		(int) 0 => 'FC003G09000'
	),
	'ptri' => array(
		(int) 0 => 'PTI_21G02570'
	),
	'nga' => array(
		(int) 0 => 'Naga_100001g67'
	),
	'phs' => array(
		(int) 0 => 'phs344240'
	),
	'ppa' => array(
		(int) 0 => 'PP00270G00460'
	),
	'osa' => array(
		(int) 0 => 'OS03G57300'
	),
	'ath' => array(
		(int) 0 => 'AT5G16280'
	),
	'atr' => array(
		(int) 0 => 'ATR_00030G00120'
	),
	'cvu' => array(
		(int) 0 => 'CV00G05540'
	),
	'mrcc299' => array(
		(int) 0 => 'MRCC299_03G08000'
	),
	'aan' => array(
		(int) 0 => 'AA0024G00080',
		(int) 1 => 'AA0026G00250'
	),
	'acg' => array(
		(int) 0 => 'AC00G45200'
	),
	'hom' => array(
		(int) 0 => 'ENSG00000153339'
	),
	'mus' => array(
		(int) 0 => 'ENSMUSG00000033382'
	),
	'esi' => array(
		(int) 0 => 'ES0205G00170',
		(int) 1 => 'ES0205G00050'
	),
	'drm' => array(
		(int) 0 => 'FBgn0260655'
	),
	'olu' => array(
		(int) 0 => 'OL17G01190'
	),
	'cre' => array(
		(int) 0 => 'CR01G05390'
	),
	'ome' => array(
		(int) 0 => 'OM_18G01010'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0292682'
	),
	'ota' => array(
		(int) 0 => 'OT_18G01170'
	),
	'orcc809' => array(
		(int) 0 => 'ORCC809_17G01190'
	),
	'vca' => array(
		(int) 0 => 'VC00G45660'
	),
	'cnc64a' => array(
		(int) 0 => 'CNC64A_003G00260',
		(int) 1 => 'CNC64A_003G00300'
	),
	'mpu' => array(
		(int) 0 => 'MP17G02120'
	),
	'pse3' => array(
		(int) 0 => 'PI00G14610'
	),
	'cel' => array(
		(int) 0 => 'WBGene00018512'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.05g02320'
	),
	'bprrcc1105' => array(
		(int) 0 => 'BPRRCC1105_09G00820'
	),
	'apr' => array(
		(int) 0 => 'AP00G64240'
	)
)
$gene_id = 'FC003G09000'
$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 = 'FC003G09000'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'MP01G04550'
$gf_placeholder = 'HOM03P020323'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_094G00020',
	'e_value' => '4e-11',
	'bit_score' => '69.7',
	'alignment_length' => '250',
	'identity_percentage' => '28.00',
	'gf' => array(
		'HOMFAM' => 'HOM03P002585',
		'ORTHOFAM' => 'ORTHO03P002556'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_094G00020'
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