Pico-PLAZA 3.0 : Interactive Phylogenetics Module

Interactive Phylogenetics Module

Gene Id: ENSG00000169609

Contact Settings

If more than 50 genes/sequences are provided as input, then the associated running time could be too to stall the browser.
Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes.
After processing you will be send an email with a link to the created phylogenetic tree.

Email Address (optional)

Genes

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(
		'ENSG00000169609' => array(
			'gene_id' => 'ENSG00000169609',
			'e_value' => '5e-116',
			'bit_score' => '333',
			'alignment_length' => '168',
			'identity_percentage' => '100.00',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0035415' => array(
			'gene_id' => 'FBgn0035415',
			'e_value' => '4e-24',
			'bit_score' => '97.1',
			'alignment_length' => '97',
			'identity_percentage' => '52.58',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte375030' => array(
			'gene_id' => 'pte375030',
			'e_value' => '3e-12',
			'bit_score' => '64.3',
			'alignment_length' => '64',
			'identity_percentage' => '43.75',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte338140' => array(
			'gene_id' => 'pte338140',
			'e_value' => '4e-12',
			'bit_score' => '63.9',
			'alignment_length' => '65',
			'identity_percentage' => '44.62',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G49170' => array(
			'gene_id' => 'AT1G49170',
			'e_value' => '1e-11',
			'bit_score' => '63.2',
			'alignment_length' => '58',
			'identity_percentage' => '53.45',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00107G00820' => array(
			'gene_id' => 'PP00107G00820',
			'e_value' => '2e-10',
			'bit_score' => '59.7',
			'alignment_length' => '58',
			'identity_percentage' => '51.72',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00012164' => array(
			'gene_id' => 'WBGene00012164',
			'e_value' => '5e-10',
			'bit_score' => '58.2',
			'alignment_length' => '65',
			'identity_percentage' => '46.15',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000178078' => array(
			'gene_id' => 'ENSG00000178078',
			'e_value' => '5e-10',
			'bit_score' => '61.2',
			'alignment_length' => '39',
			'identity_percentage' => '76.92',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS04G58970' => array(
			'gene_id' => 'OS04G58970',
			'e_value' => '2e-09',
			'bit_score' => '56.6',
			'alignment_length' => '60',
			'identity_percentage' => '48.33',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00030G00510' => array(
			'gene_id' => 'ATR_00030G00510',
			'e_value' => '2e-09',
			'bit_score' => '56.2',
			'alignment_length' => '57',
			'identity_percentage' => '43.86',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000197734' => array(
			'gene_id' => 'ENSG00000197734',
			'e_value' => '3e-09',
			'bit_score' => '55.8',
			'alignment_length' => '40',
			'identity_percentage' => '72.50',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000241043' => array(
			'gene_id' => 'ENSG00000241043',
			'e_value' => '4e-09',
			'bit_score' => '56.6',
			'alignment_length' => '45',
			'identity_percentage' => '62.22',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000005801' => array(
			'gene_id' => 'ENSG00000005801',
			'e_value' => '1e-08',
			'bit_score' => '57.0',
			'alignment_length' => '41',
			'identity_percentage' => '68.29',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_044G00090' => array(
			'gene_id' => 'CNC64A_044G00090',
			'e_value' => '1e-08',
			'bit_score' => '53.9',
			'alignment_length' => '69',
			'identity_percentage' => '44.93',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS04G58980' => array(
			'gene_id' => 'OS04G58980',
			'e_value' => '3e-08',
			'bit_score' => '56.2',
			'alignment_length' => '60',
			'identity_percentage' => '48.33',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000280226' => array(
			'gene_id' => 'ENSG00000280226',
			'e_value' => '3e-08',
			'bit_score' => '52.0',
			'alignment_length' => '48',
			'identity_percentage' => '58.33',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000281835' => array(
			'gene_id' => 'ENSG00000281835',
			'e_value' => '3e-08',
			'bit_score' => '52.0',
			'alignment_length' => '48',
			'identity_percentage' => '58.33',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G00630' => array(
			'gene_id' => 'AP00G00630',
			'e_value' => '7e-08',
			'bit_score' => '54.7',
			'alignment_length' => '89',
			'identity_percentage' => '40.45',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000167562' => array(
			'gene_id' => 'ENSG00000167562',
			'e_value' => '1e-07',
			'bit_score' => '53.9',
			'alignment_length' => '37',
			'identity_percentage' => '70.27',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00013G01680' => array(
			'gene_id' => 'ATR_00013G01680',
			'e_value' => '2e-07',
			'bit_score' => '52.8',
			'alignment_length' => '90',
			'identity_percentage' => '32.22',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000279244' => array(
			'gene_id' => 'ENSG00000279244',
			'e_value' => '2e-07',
			'bit_score' => '50.1',
			'alignment_length' => '50',
			'identity_percentage' => '52.00',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000179240' => array(
			'gene_id' => 'ENSG00000179240',
			'e_value' => '3e-07',
			'bit_score' => '52.4',
			'alignment_length' => '89',
			'identity_percentage' => '39.33',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000278883' => array(
			'gene_id' => 'ENSG00000278883',
			'e_value' => '3e-07',
			'bit_score' => '48.9',
			'alignment_length' => '35',
			'identity_percentage' => '71.43',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS07G19470' => array(
			'gene_id' => 'OS07G19470',
			'e_value' => '4e-07',
			'bit_score' => '51.6',
			'alignment_length' => '90',
			'identity_percentage' => '33.33',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT5G63440' => array(
			'gene_id' => 'AT5G63440',
			'e_value' => '4e-07',
			'bit_score' => '51.6',
			'alignment_length' => '90',
			'identity_percentage' => '32.22',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000280550' => array(
			'gene_id' => 'ENSG00000280550',
			'e_value' => '5e-07',
			'bit_score' => '48.5',
			'alignment_length' => '31',
			'identity_percentage' => '77.42',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00003G01010' => array(
			'gene_id' => 'PP00003G01010',
			'e_value' => '5e-07',
			'bit_score' => '51.2',
			'alignment_length' => '90',
			'identity_percentage' => '32.22',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00121G00070' => array(
			'gene_id' => 'PP00121G00070',
			'e_value' => '2e-06',
			'bit_score' => '50.1',
			'alignment_length' => '90',
			'identity_percentage' => '31.11',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu22520' => array(
			'gene_id' => 'gsu22520',
			'e_value' => '3e-06',
			'bit_score' => '47.8',
			'alignment_length' => '62',
			'identity_percentage' => '37.10',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000170456' => array(
			'gene_id' => 'ENSG00000170456',
			'e_value' => '6e-06',
			'bit_score' => '49.3',
			'alignment_length' => '37',
			'identity_percentage' => '64.86',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'hom' => array(
			(int) 0 => 'ENSG00000169609',
			(int) 1 => 'ENSG00000178078',
			(int) 2 => 'ENSG00000197734',
			(int) 3 => 'ENSG00000241043',
			(int) 4 => 'ENSG00000005801',
			(int) 5 => 'ENSG00000280226',
			(int) 6 => 'ENSG00000281835',
			(int) 7 => 'ENSG00000167562',
			(int) 8 => 'ENSG00000279244',
			(int) 9 => 'ENSG00000179240',
			(int) 10 => 'ENSG00000278883',
			(int) 11 => 'ENSG00000280550',
			(int) 12 => 'ENSG00000170456'
		),
		'drm' => array(
			(int) 0 => 'FBgn0035415'
		),
		'pte' => array(
			(int) 0 => 'pte375030',
			(int) 1 => 'pte338140'
		),
		'ath' => array(
			(int) 0 => 'AT1G49170',
			(int) 1 => 'AT5G63440'
		),
		'ppa' => array(
			(int) 0 => 'PP00107G00820',
			(int) 1 => 'PP00003G01010',
			(int) 2 => 'PP00121G00070'
		),
		'cel' => array(
			(int) 0 => 'WBGene00012164'
		),
		'osa' => array(
			(int) 0 => 'OS04G58970',
			(int) 1 => 'OS04G58980',
			(int) 2 => 'OS07G19470'
		),
		'atr' => array(
			(int) 0 => 'ATR_00030G00510',
			(int) 1 => 'ATR_00013G01680'
		),
		'apr' => array(
			(int) 0 => 'AP00G00630'
		),
		'gsu' => array(
			(int) 0 => 'gsu22520'
		)
	),
	'gene_id' => 'ENSG00000169609',
	'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' => 'ENSG00000169609',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'SPRRNA.32',
	'gf_placeholder' => 'HOM03P021710',
	'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(
	'ENSG00000169609' => array(
		'gene_id' => 'ENSG00000169609',
		'e_value' => '5e-116',
		'bit_score' => '333',
		'alignment_length' => '168',
		'identity_percentage' => '100.00',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'FBgn0035415' => array(
		'gene_id' => 'FBgn0035415',
		'e_value' => '4e-24',
		'bit_score' => '97.1',
		'alignment_length' => '97',
		'identity_percentage' => '52.58',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'pte375030' => array(
		'gene_id' => 'pte375030',
		'e_value' => '3e-12',
		'bit_score' => '64.3',
		'alignment_length' => '64',
		'identity_percentage' => '43.75',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'pte338140' => array(
		'gene_id' => 'pte338140',
		'e_value' => '4e-12',
		'bit_score' => '63.9',
		'alignment_length' => '65',
		'identity_percentage' => '44.62',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'AT1G49170' => array(
		'gene_id' => 'AT1G49170',
		'e_value' => '1e-11',
		'bit_score' => '63.2',
		'alignment_length' => '58',
		'identity_percentage' => '53.45',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'PP00107G00820' => array(
		'gene_id' => 'PP00107G00820',
		'e_value' => '2e-10',
		'bit_score' => '59.7',
		'alignment_length' => '58',
		'identity_percentage' => '51.72',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'WBGene00012164' => array(
		'gene_id' => 'WBGene00012164',
		'e_value' => '5e-10',
		'bit_score' => '58.2',
		'alignment_length' => '65',
		'identity_percentage' => '46.15',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'ENSG00000178078' => array(
		'gene_id' => 'ENSG00000178078',
		'e_value' => '5e-10',
		'bit_score' => '61.2',
		'alignment_length' => '39',
		'identity_percentage' => '76.92',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P021290',
			'ORTHOFAM' => 'ORTHO03P074392'
		)
	),
	'OS04G58970' => array(
		'gene_id' => 'OS04G58970',
		'e_value' => '2e-09',
		'bit_score' => '56.6',
		'alignment_length' => '60',
		'identity_percentage' => '48.33',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'ATR_00030G00510' => array(
		'gene_id' => 'ATR_00030G00510',
		'e_value' => '2e-09',
		'bit_score' => '56.2',
		'alignment_length' => '57',
		'identity_percentage' => '43.86',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'ENSG00000197734' => array(
		'gene_id' => 'ENSG00000197734',
		'e_value' => '3e-09',
		'bit_score' => '55.8',
		'alignment_length' => '40',
		'identity_percentage' => '72.50',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000241043' => array(
		'gene_id' => 'ENSG00000241043',
		'e_value' => '4e-09',
		'bit_score' => '56.6',
		'alignment_length' => '45',
		'identity_percentage' => '62.22',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000005801' => array(
		'gene_id' => 'ENSG00000005801',
		'e_value' => '1e-08',
		'bit_score' => '57.0',
		'alignment_length' => '41',
		'identity_percentage' => '68.29',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000007',
			'ORTHOFAM' => 'ORTHO03P169941'
		)
	),
	'CNC64A_044G00090' => array(
		'gene_id' => 'CNC64A_044G00090',
		'e_value' => '1e-08',
		'bit_score' => '53.9',
		'alignment_length' => '69',
		'identity_percentage' => '44.93',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'OS04G58980' => array(
		'gene_id' => 'OS04G58980',
		'e_value' => '3e-08',
		'bit_score' => '56.2',
		'alignment_length' => '60',
		'identity_percentage' => '48.33',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000026',
			'ORTHOFAM' => 'ORTHO03P075671'
		)
	),
	'ENSG00000280226' => array(
		'gene_id' => 'ENSG00000280226',
		'e_value' => '3e-08',
		'bit_score' => '52.0',
		'alignment_length' => '48',
		'identity_percentage' => '58.33',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000281835' => array(
		'gene_id' => 'ENSG00000281835',
		'e_value' => '3e-08',
		'bit_score' => '52.0',
		'alignment_length' => '48',
		'identity_percentage' => '58.33',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'AP00G00630' => array(
		'gene_id' => 'AP00G00630',
		'e_value' => '7e-08',
		'bit_score' => '54.7',
		'alignment_length' => '89',
		'identity_percentage' => '40.45',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ENSG00000167562' => array(
		'gene_id' => 'ENSG00000167562',
		'e_value' => '1e-07',
		'bit_score' => '53.9',
		'alignment_length' => '37',
		'identity_percentage' => '70.27',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000007',
			'ORTHOFAM' => 'ORTHO03P008850'
		)
	),
	'ATR_00013G01680' => array(
		'gene_id' => 'ATR_00013G01680',
		'e_value' => '2e-07',
		'bit_score' => '52.8',
		'alignment_length' => '90',
		'identity_percentage' => '32.22',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'ENSG00000279244' => array(
		'gene_id' => 'ENSG00000279244',
		'e_value' => '2e-07',
		'bit_score' => '50.1',
		'alignment_length' => '50',
		'identity_percentage' => '52.00',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000179240' => array(
		'gene_id' => 'ENSG00000179240',
		'e_value' => '3e-07',
		'bit_score' => '52.4',
		'alignment_length' => '89',
		'identity_percentage' => '39.33',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000278883' => array(
		'gene_id' => 'ENSG00000278883',
		'e_value' => '3e-07',
		'bit_score' => '48.9',
		'alignment_length' => '35',
		'identity_percentage' => '71.43',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'OS07G19470' => array(
		'gene_id' => 'OS07G19470',
		'e_value' => '4e-07',
		'bit_score' => '51.6',
		'alignment_length' => '90',
		'identity_percentage' => '33.33',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'AT5G63440' => array(
		'gene_id' => 'AT5G63440',
		'e_value' => '4e-07',
		'bit_score' => '51.6',
		'alignment_length' => '90',
		'identity_percentage' => '32.22',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'ENSG00000280550' => array(
		'gene_id' => 'ENSG00000280550',
		'e_value' => '5e-07',
		'bit_score' => '48.5',
		'alignment_length' => '31',
		'identity_percentage' => '77.42',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'PP00003G01010' => array(
		'gene_id' => 'PP00003G01010',
		'e_value' => '5e-07',
		'bit_score' => '51.2',
		'alignment_length' => '90',
		'identity_percentage' => '32.22',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'PP00121G00070' => array(
		'gene_id' => 'PP00121G00070',
		'e_value' => '2e-06',
		'bit_score' => '50.1',
		'alignment_length' => '90',
		'identity_percentage' => '31.11',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'gsu22520' => array(
		'gene_id' => 'gsu22520',
		'e_value' => '3e-06',
		'bit_score' => '47.8',
		'alignment_length' => '62',
		'identity_percentage' => '37.10',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P025214',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'ENSG00000170456' => array(
		'gene_id' => 'ENSG00000170456',
		'e_value' => '6e-06',
		'bit_score' => '49.3',
		'alignment_length' => '37',
		'identity_percentage' => '64.86',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002025',
			'ORTHOFAM' => 'ORTHO03P019424'
		)
	)
)
$similarity_hits_species = array(
	'hom' => array(
		(int) 0 => 'ENSG00000169609',
		(int) 1 => 'ENSG00000178078',
		(int) 2 => 'ENSG00000197734',
		(int) 3 => 'ENSG00000241043',
		(int) 4 => 'ENSG00000005801',
		(int) 5 => 'ENSG00000280226',
		(int) 6 => 'ENSG00000281835',
		(int) 7 => 'ENSG00000167562',
		(int) 8 => 'ENSG00000279244',
		(int) 9 => 'ENSG00000179240',
		(int) 10 => 'ENSG00000278883',
		(int) 11 => 'ENSG00000280550',
		(int) 12 => 'ENSG00000170456'
	),
	'drm' => array(
		(int) 0 => 'FBgn0035415'
	),
	'pte' => array(
		(int) 0 => 'pte375030',
		(int) 1 => 'pte338140'
	),
	'ath' => array(
		(int) 0 => 'AT1G49170',
		(int) 1 => 'AT5G63440'
	),
	'ppa' => array(
		(int) 0 => 'PP00107G00820',
		(int) 1 => 'PP00003G01010',
		(int) 2 => 'PP00121G00070'
	),
	'cel' => array(
		(int) 0 => 'WBGene00012164'
	),
	'osa' => array(
		(int) 0 => 'OS04G58970',
		(int) 1 => 'OS04G58980',
		(int) 2 => 'OS07G19470'
	),
	'atr' => array(
		(int) 0 => 'ATR_00030G00510',
		(int) 1 => 'ATR_00013G01680'
	),
	'apr' => array(
		(int) 0 => 'AP00G00630'
	),
	'gsu' => array(
		(int) 0 => 'gsu22520'
	)
)
$gene_id = 'ENSG00000169609'
$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 = 'ENSG00000169609'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'SPRRNA.32'
$gf_placeholder = 'HOM03P021710'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_044G00090',
	'e_value' => '1e-08',
	'bit_score' => '53.9',
	'alignment_length' => '69',
	'identity_percentage' => '44.93',
	'gf' => array(
		'HOMFAM' => 'HOM03P007129',
		'ORTHOFAM' => 'ORTHO03P006507'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00090'
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(
		'ENSG00000169609' => array(
			'gene_id' => 'ENSG00000169609',
			'e_value' => '5e-116',
			'bit_score' => '333',
			'alignment_length' => '168',
			'identity_percentage' => '100.00',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0035415' => array(
			'gene_id' => 'FBgn0035415',
			'e_value' => '4e-24',
			'bit_score' => '97.1',
			'alignment_length' => '97',
			'identity_percentage' => '52.58',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte375030' => array(
			'gene_id' => 'pte375030',
			'e_value' => '3e-12',
			'bit_score' => '64.3',
			'alignment_length' => '64',
			'identity_percentage' => '43.75',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte338140' => array(
			'gene_id' => 'pte338140',
			'e_value' => '4e-12',
			'bit_score' => '63.9',
			'alignment_length' => '65',
			'identity_percentage' => '44.62',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G49170' => array(
			'gene_id' => 'AT1G49170',
			'e_value' => '1e-11',
			'bit_score' => '63.2',
			'alignment_length' => '58',
			'identity_percentage' => '53.45',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00107G00820' => array(
			'gene_id' => 'PP00107G00820',
			'e_value' => '2e-10',
			'bit_score' => '59.7',
			'alignment_length' => '58',
			'identity_percentage' => '51.72',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00012164' => array(
			'gene_id' => 'WBGene00012164',
			'e_value' => '5e-10',
			'bit_score' => '58.2',
			'alignment_length' => '65',
			'identity_percentage' => '46.15',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000178078' => array(
			'gene_id' => 'ENSG00000178078',
			'e_value' => '5e-10',
			'bit_score' => '61.2',
			'alignment_length' => '39',
			'identity_percentage' => '76.92',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS04G58970' => array(
			'gene_id' => 'OS04G58970',
			'e_value' => '2e-09',
			'bit_score' => '56.6',
			'alignment_length' => '60',
			'identity_percentage' => '48.33',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00030G00510' => array(
			'gene_id' => 'ATR_00030G00510',
			'e_value' => '2e-09',
			'bit_score' => '56.2',
			'alignment_length' => '57',
			'identity_percentage' => '43.86',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000197734' => array(
			'gene_id' => 'ENSG00000197734',
			'e_value' => '3e-09',
			'bit_score' => '55.8',
			'alignment_length' => '40',
			'identity_percentage' => '72.50',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000241043' => array(
			'gene_id' => 'ENSG00000241043',
			'e_value' => '4e-09',
			'bit_score' => '56.6',
			'alignment_length' => '45',
			'identity_percentage' => '62.22',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000005801' => array(
			'gene_id' => 'ENSG00000005801',
			'e_value' => '1e-08',
			'bit_score' => '57.0',
			'alignment_length' => '41',
			'identity_percentage' => '68.29',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_044G00090' => array(
			'gene_id' => 'CNC64A_044G00090',
			'e_value' => '1e-08',
			'bit_score' => '53.9',
			'alignment_length' => '69',
			'identity_percentage' => '44.93',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS04G58980' => array(
			'gene_id' => 'OS04G58980',
			'e_value' => '3e-08',
			'bit_score' => '56.2',
			'alignment_length' => '60',
			'identity_percentage' => '48.33',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000280226' => array(
			'gene_id' => 'ENSG00000280226',
			'e_value' => '3e-08',
			'bit_score' => '52.0',
			'alignment_length' => '48',
			'identity_percentage' => '58.33',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000281835' => array(
			'gene_id' => 'ENSG00000281835',
			'e_value' => '3e-08',
			'bit_score' => '52.0',
			'alignment_length' => '48',
			'identity_percentage' => '58.33',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G00630' => array(
			'gene_id' => 'AP00G00630',
			'e_value' => '7e-08',
			'bit_score' => '54.7',
			'alignment_length' => '89',
			'identity_percentage' => '40.45',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000167562' => array(
			'gene_id' => 'ENSG00000167562',
			'e_value' => '1e-07',
			'bit_score' => '53.9',
			'alignment_length' => '37',
			'identity_percentage' => '70.27',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00013G01680' => array(
			'gene_id' => 'ATR_00013G01680',
			'e_value' => '2e-07',
			'bit_score' => '52.8',
			'alignment_length' => '90',
			'identity_percentage' => '32.22',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000279244' => array(
			'gene_id' => 'ENSG00000279244',
			'e_value' => '2e-07',
			'bit_score' => '50.1',
			'alignment_length' => '50',
			'identity_percentage' => '52.00',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000179240' => array(
			'gene_id' => 'ENSG00000179240',
			'e_value' => '3e-07',
			'bit_score' => '52.4',
			'alignment_length' => '89',
			'identity_percentage' => '39.33',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000278883' => array(
			'gene_id' => 'ENSG00000278883',
			'e_value' => '3e-07',
			'bit_score' => '48.9',
			'alignment_length' => '35',
			'identity_percentage' => '71.43',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS07G19470' => array(
			'gene_id' => 'OS07G19470',
			'e_value' => '4e-07',
			'bit_score' => '51.6',
			'alignment_length' => '90',
			'identity_percentage' => '33.33',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT5G63440' => array(
			'gene_id' => 'AT5G63440',
			'e_value' => '4e-07',
			'bit_score' => '51.6',
			'alignment_length' => '90',
			'identity_percentage' => '32.22',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000280550' => array(
			'gene_id' => 'ENSG00000280550',
			'e_value' => '5e-07',
			'bit_score' => '48.5',
			'alignment_length' => '31',
			'identity_percentage' => '77.42',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00003G01010' => array(
			'gene_id' => 'PP00003G01010',
			'e_value' => '5e-07',
			'bit_score' => '51.2',
			'alignment_length' => '90',
			'identity_percentage' => '32.22',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00121G00070' => array(
			'gene_id' => 'PP00121G00070',
			'e_value' => '2e-06',
			'bit_score' => '50.1',
			'alignment_length' => '90',
			'identity_percentage' => '31.11',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu22520' => array(
			'gene_id' => 'gsu22520',
			'e_value' => '3e-06',
			'bit_score' => '47.8',
			'alignment_length' => '62',
			'identity_percentage' => '37.10',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSG00000170456' => array(
			'gene_id' => 'ENSG00000170456',
			'e_value' => '6e-06',
			'bit_score' => '49.3',
			'alignment_length' => '37',
			'identity_percentage' => '64.86',
			'species' => 'hom',
			'common_name' => 'Homo sapiens',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'hom' => array(
			(int) 0 => 'ENSG00000169609',
			(int) 1 => 'ENSG00000178078',
			(int) 2 => 'ENSG00000197734',
			(int) 3 => 'ENSG00000241043',
			(int) 4 => 'ENSG00000005801',
			(int) 5 => 'ENSG00000280226',
			(int) 6 => 'ENSG00000281835',
			(int) 7 => 'ENSG00000167562',
			(int) 8 => 'ENSG00000279244',
			(int) 9 => 'ENSG00000179240',
			(int) 10 => 'ENSG00000278883',
			(int) 11 => 'ENSG00000280550',
			(int) 12 => 'ENSG00000170456'
		),
		'drm' => array(
			(int) 0 => 'FBgn0035415'
		),
		'pte' => array(
			(int) 0 => 'pte375030',
			(int) 1 => 'pte338140'
		),
		'ath' => array(
			(int) 0 => 'AT1G49170',
			(int) 1 => 'AT5G63440'
		),
		'ppa' => array(
			(int) 0 => 'PP00107G00820',
			(int) 1 => 'PP00003G01010',
			(int) 2 => 'PP00121G00070'
		),
		'cel' => array(
			(int) 0 => 'WBGene00012164'
		),
		'osa' => array(
			(int) 0 => 'OS04G58970',
			(int) 1 => 'OS04G58980',
			(int) 2 => 'OS07G19470'
		),
		'atr' => array(
			(int) 0 => 'ATR_00030G00510',
			(int) 1 => 'ATR_00013G01680'
		),
		'apr' => array(
			(int) 0 => 'AP00G00630'
		),
		'gsu' => array(
			(int) 0 => 'gsu22520'
		)
	),
	'gene_id' => 'ENSG00000169609',
	'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' => 'ENSG00000169609',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'SPRRNA.32',
	'gf_placeholder' => 'HOM03P021710',
	'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(
	'ENSG00000169609' => array(
		'gene_id' => 'ENSG00000169609',
		'e_value' => '5e-116',
		'bit_score' => '333',
		'alignment_length' => '168',
		'identity_percentage' => '100.00',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'FBgn0035415' => array(
		'gene_id' => 'FBgn0035415',
		'e_value' => '4e-24',
		'bit_score' => '97.1',
		'alignment_length' => '97',
		'identity_percentage' => '52.58',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'pte375030' => array(
		'gene_id' => 'pte375030',
		'e_value' => '3e-12',
		'bit_score' => '64.3',
		'alignment_length' => '64',
		'identity_percentage' => '43.75',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'pte338140' => array(
		'gene_id' => 'pte338140',
		'e_value' => '4e-12',
		'bit_score' => '63.9',
		'alignment_length' => '65',
		'identity_percentage' => '44.62',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'AT1G49170' => array(
		'gene_id' => 'AT1G49170',
		'e_value' => '1e-11',
		'bit_score' => '63.2',
		'alignment_length' => '58',
		'identity_percentage' => '53.45',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'PP00107G00820' => array(
		'gene_id' => 'PP00107G00820',
		'e_value' => '2e-10',
		'bit_score' => '59.7',
		'alignment_length' => '58',
		'identity_percentage' => '51.72',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'WBGene00012164' => array(
		'gene_id' => 'WBGene00012164',
		'e_value' => '5e-10',
		'bit_score' => '58.2',
		'alignment_length' => '65',
		'identity_percentage' => '46.15',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'ENSG00000178078' => array(
		'gene_id' => 'ENSG00000178078',
		'e_value' => '5e-10',
		'bit_score' => '61.2',
		'alignment_length' => '39',
		'identity_percentage' => '76.92',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P021290',
			'ORTHOFAM' => 'ORTHO03P074392'
		)
	),
	'OS04G58970' => array(
		'gene_id' => 'OS04G58970',
		'e_value' => '2e-09',
		'bit_score' => '56.6',
		'alignment_length' => '60',
		'identity_percentage' => '48.33',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'ATR_00030G00510' => array(
		'gene_id' => 'ATR_00030G00510',
		'e_value' => '2e-09',
		'bit_score' => '56.2',
		'alignment_length' => '57',
		'identity_percentage' => '43.86',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'ENSG00000197734' => array(
		'gene_id' => 'ENSG00000197734',
		'e_value' => '3e-09',
		'bit_score' => '55.8',
		'alignment_length' => '40',
		'identity_percentage' => '72.50',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000241043' => array(
		'gene_id' => 'ENSG00000241043',
		'e_value' => '4e-09',
		'bit_score' => '56.6',
		'alignment_length' => '45',
		'identity_percentage' => '62.22',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000005801' => array(
		'gene_id' => 'ENSG00000005801',
		'e_value' => '1e-08',
		'bit_score' => '57.0',
		'alignment_length' => '41',
		'identity_percentage' => '68.29',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000007',
			'ORTHOFAM' => 'ORTHO03P169941'
		)
	),
	'CNC64A_044G00090' => array(
		'gene_id' => 'CNC64A_044G00090',
		'e_value' => '1e-08',
		'bit_score' => '53.9',
		'alignment_length' => '69',
		'identity_percentage' => '44.93',
		'gf' => array(
			'HOMFAM' => 'HOM03P007129',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'OS04G58980' => array(
		'gene_id' => 'OS04G58980',
		'e_value' => '3e-08',
		'bit_score' => '56.2',
		'alignment_length' => '60',
		'identity_percentage' => '48.33',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000026',
			'ORTHOFAM' => 'ORTHO03P075671'
		)
	),
	'ENSG00000280226' => array(
		'gene_id' => 'ENSG00000280226',
		'e_value' => '3e-08',
		'bit_score' => '52.0',
		'alignment_length' => '48',
		'identity_percentage' => '58.33',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000281835' => array(
		'gene_id' => 'ENSG00000281835',
		'e_value' => '3e-08',
		'bit_score' => '52.0',
		'alignment_length' => '48',
		'identity_percentage' => '58.33',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'AP00G00630' => array(
		'gene_id' => 'AP00G00630',
		'e_value' => '7e-08',
		'bit_score' => '54.7',
		'alignment_length' => '89',
		'identity_percentage' => '40.45',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001586',
			'ORTHOFAM' => 'ORTHO03P000813'
		)
	),
	'ENSG00000167562' => array(
		'gene_id' => 'ENSG00000167562',
		'e_value' => '1e-07',
		'bit_score' => '53.9',
		'alignment_length' => '37',
		'identity_percentage' => '70.27',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000007',
			'ORTHOFAM' => 'ORTHO03P008850'
		)
	),
	'ATR_00013G01680' => array(
		'gene_id' => 'ATR_00013G01680',
		'e_value' => '2e-07',
		'bit_score' => '52.8',
		'alignment_length' => '90',
		'identity_percentage' => '32.22',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'ENSG00000279244' => array(
		'gene_id' => 'ENSG00000279244',
		'e_value' => '2e-07',
		'bit_score' => '50.1',
		'alignment_length' => '50',
		'identity_percentage' => '52.00',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000179240' => array(
		'gene_id' => 'ENSG00000179240',
		'e_value' => '3e-07',
		'bit_score' => '52.4',
		'alignment_length' => '89',
		'identity_percentage' => '39.33',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'ENSG00000278883' => array(
		'gene_id' => 'ENSG00000278883',
		'e_value' => '3e-07',
		'bit_score' => '48.9',
		'alignment_length' => '35',
		'identity_percentage' => '71.43',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'OS07G19470' => array(
		'gene_id' => 'OS07G19470',
		'e_value' => '4e-07',
		'bit_score' => '51.6',
		'alignment_length' => '90',
		'identity_percentage' => '33.33',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'AT5G63440' => array(
		'gene_id' => 'AT5G63440',
		'e_value' => '4e-07',
		'bit_score' => '51.6',
		'alignment_length' => '90',
		'identity_percentage' => '32.22',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'ENSG00000280550' => array(
		'gene_id' => 'ENSG00000280550',
		'e_value' => '5e-07',
		'bit_score' => '48.5',
		'alignment_length' => '31',
		'identity_percentage' => '77.42',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P007087',
			'ORTHOFAM' => 'ORTHO03P010210'
		)
	),
	'PP00003G01010' => array(
		'gene_id' => 'PP00003G01010',
		'e_value' => '5e-07',
		'bit_score' => '51.2',
		'alignment_length' => '90',
		'identity_percentage' => '32.22',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'PP00121G00070' => array(
		'gene_id' => 'PP00121G00070',
		'e_value' => '2e-06',
		'bit_score' => '50.1',
		'alignment_length' => '90',
		'identity_percentage' => '31.11',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P003998',
			'ORTHOFAM' => 'ORTHO03P003823'
		)
	),
	'gsu22520' => array(
		'gene_id' => 'gsu22520',
		'e_value' => '3e-06',
		'bit_score' => '47.8',
		'alignment_length' => '62',
		'identity_percentage' => '37.10',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P025214',
			'ORTHOFAM' => 'ORTHO03P006507'
		)
	),
	'ENSG00000170456' => array(
		'gene_id' => 'ENSG00000170456',
		'e_value' => '6e-06',
		'bit_score' => '49.3',
		'alignment_length' => '37',
		'identity_percentage' => '64.86',
		'species' => 'hom',
		'common_name' => 'Homo sapiens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002025',
			'ORTHOFAM' => 'ORTHO03P019424'
		)
	)
)
$similarity_hits_species = array(
	'hom' => array(
		(int) 0 => 'ENSG00000169609',
		(int) 1 => 'ENSG00000178078',
		(int) 2 => 'ENSG00000197734',
		(int) 3 => 'ENSG00000241043',
		(int) 4 => 'ENSG00000005801',
		(int) 5 => 'ENSG00000280226',
		(int) 6 => 'ENSG00000281835',
		(int) 7 => 'ENSG00000167562',
		(int) 8 => 'ENSG00000279244',
		(int) 9 => 'ENSG00000179240',
		(int) 10 => 'ENSG00000278883',
		(int) 11 => 'ENSG00000280550',
		(int) 12 => 'ENSG00000170456'
	),
	'drm' => array(
		(int) 0 => 'FBgn0035415'
	),
	'pte' => array(
		(int) 0 => 'pte375030',
		(int) 1 => 'pte338140'
	),
	'ath' => array(
		(int) 0 => 'AT1G49170',
		(int) 1 => 'AT5G63440'
	),
	'ppa' => array(
		(int) 0 => 'PP00107G00820',
		(int) 1 => 'PP00003G01010',
		(int) 2 => 'PP00121G00070'
	),
	'cel' => array(
		(int) 0 => 'WBGene00012164'
	),
	'osa' => array(
		(int) 0 => 'OS04G58970',
		(int) 1 => 'OS04G58980',
		(int) 2 => 'OS07G19470'
	),
	'atr' => array(
		(int) 0 => 'ATR_00030G00510',
		(int) 1 => 'ATR_00013G01680'
	),
	'apr' => array(
		(int) 0 => 'AP00G00630'
	),
	'gsu' => array(
		(int) 0 => 'gsu22520'
	)
)
$gene_id = 'ENSG00000169609'
$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 = 'ENSG00000169609'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'SPRRNA.32'
$gf_placeholder = 'HOM03P021710'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_044G00090',
	'e_value' => '1e-08',
	'bit_score' => '53.9',
	'alignment_length' => '69',
	'identity_percentage' => '44.93',
	'gf' => array(
		'HOMFAM' => 'HOM03P007129',
		'ORTHOFAM' => 'ORTHO03P006507'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00090'
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

Gene ID	Organism	E-value	Bitscore	Alignment Length	Identity Percentage
ENSG00000169609	Homo sapiens	5e-116	333	168	100.00
FBgn0035415	Drosophila melanogaster	4e-24	97.1	97	52.58
pte375030	Paramecium tetraurelia	3e-12	64.3	64	43.75
pte338140	Paramecium tetraurelia	4e-12	63.9	65	44.62
AT1G49170	Arabidopsis thaliana	1e-11	63.2	58	53.45
PP00107G00820	Physcomitrella patens	2e-10	59.7	58	51.72
WBGene00012164	Caenorhabditis elegans	5e-10	58.2	65	46.15
ENSG00000178078	Homo sapiens	5e-10	61.2	39	76.92
OS04G58970	Oryza sativa	2e-09	56.6	60	48.33
ATR_00030G00510	Amborella trichopoda	2e-09	56.2	57	43.86
ENSG00000197734	Homo sapiens	3e-09	55.8	40	72.50
ENSG00000241043	Homo sapiens	4e-09	56.6	45	62.22
ENSG00000005801	Homo sapiens	1e-08	57.0	41	68.29
CNC64A_044G00090		1e-08	53.9	69	44.93
OS04G58980	Oryza sativa	3e-08	56.2	60	48.33
ENSG00000280226	Homo sapiens	3e-08	52.0	48	58.33
ENSG00000281835	Homo sapiens	3e-08	52.0	48	58.33
AP00G00630	Auxenochlorella protothecoides	7e-08	54.7	89	40.45
ENSG00000167562	Homo sapiens	1e-07	53.9	37	70.27
ATR_00013G01680	Amborella trichopoda	2e-07	52.8	90	32.22
ENSG00000279244	Homo sapiens	2e-07	50.1	50	52.00
ENSG00000179240	Homo sapiens	3e-07	52.4	89	39.33
ENSG00000278883	Homo sapiens	3e-07	48.9	35	71.43
OS07G19470	Oryza sativa	4e-07	51.6	90	33.33
AT5G63440	Arabidopsis thaliana	4e-07	51.6	90	32.22
ENSG00000280550	Homo sapiens	5e-07	48.5	31	77.42
PP00003G01010	Physcomitrella patens	5e-07	51.2	90	32.22
PP00121G00070	Physcomitrella patens	2e-06	50.1	90	31.11
gsu22520	Galdieria sulphuraria	3e-06	47.8	62	37.10
ENSG00000170456	Homo sapiens	6e-06	49.3	37	64.86

External Sequences (optional)

External Sequences Type

Program Settings

MSA algorithm
Tree construction algorithm
Edit MSA alignment