Pico-PLAZA 3.0 : Interactive Phylogenetics Module

Interactive Phylogenetics Module

Gene Id: emh706320

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(
		'emh706320' => array(
			'gene_id' => 'emh706320',
			'e_value' => '0.0',
			'bit_score' => '538',
			'alignment_length' => '268',
			'identity_percentage' => '100.00',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh197970' => array(
			'gene_id' => 'emh197970',
			'e_value' => '1e-128',
			'bit_score' => '373',
			'alignment_length' => '250',
			'identity_percentage' => '80.80',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_13G02030' => array(
			'gene_id' => 'PTI_13G02030',
			'e_value' => '1e-70',
			'bit_score' => '225',
			'alignment_length' => '219',
			'identity_percentage' => '58.45',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP10G00800' => array(
			'gene_id' => 'TP10G00800',
			'e_value' => '5e-56',
			'bit_score' => '188',
			'alignment_length' => '220',
			'identity_percentage' => '48.18',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC003G02470' => array(
			'gene_id' => 'FC003G02470',
			'e_value' => '4e-46',
			'bit_score' => '160',
			'alignment_length' => '220',
			'identity_percentage' => '43.64',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh584420' => array(
			'gene_id' => 'emh584420',
			'e_value' => '3e-29',
			'bit_score' => '115',
			'alignment_length' => '228',
			'identity_percentage' => '36.84',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC002G00620' => array(
			'gene_id' => 'FC002G00620',
			'e_value' => '4e-26',
			'bit_score' => '108',
			'alignment_length' => '217',
			'identity_percentage' => '32.26',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_04G01420' => array(
			'gene_id' => 'PTI_04G01420',
			'e_value' => '5e-24',
			'bit_score' => '102',
			'alignment_length' => '224',
			'identity_percentage' => '33.48',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh134760' => array(
			'gene_id' => 'emh134760',
			'e_value' => '1e-20',
			'bit_score' => '92.8',
			'alignment_length' => '233',
			'identity_percentage' => '30.90',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP02G09850' => array(
			'gene_id' => 'TP02G09850',
			'e_value' => '3e-19',
			'bit_score' => '92.4',
			'alignment_length' => '217',
			'identity_percentage' => '31.34',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0004G02790' => array(
			'gene_id' => 'AA0004G02790',
			'e_value' => '2e-15',
			'bit_score' => '76.3',
			'alignment_length' => '221',
			'identity_percentage' => '28.96',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP03G07790' => array(
			'gene_id' => 'TP03G07790',
			'e_value' => '9e-15',
			'bit_score' => '78.2',
			'alignment_length' => '222',
			'identity_percentage' => '30.18',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh316230' => array(
			'gene_id' => 'emh316230',
			'e_value' => '2e-13',
			'bit_score' => '73.6',
			'alignment_length' => '225',
			'identity_percentage' => '28.44',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh292560' => array(
			'gene_id' => 'emh292560',
			'e_value' => '6e-13',
			'bit_score' => '70.5',
			'alignment_length' => '165',
			'identity_percentage' => '33.33',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh543440' => array(
			'gene_id' => 'emh543440',
			'e_value' => '6e-13',
			'bit_score' => '70.5',
			'alignment_length' => '165',
			'identity_percentage' => '33.33',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh469180' => array(
			'gene_id' => 'emh469180',
			'e_value' => '5e-12',
			'bit_score' => '67.0',
			'alignment_length' => '216',
			'identity_percentage' => '29.63',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.02g05280' => array(
			'gene_id' => 'RCC4223.02g05280',
			'e_value' => '5e-12',
			'bit_score' => '67.4',
			'alignment_length' => '226',
			'identity_percentage' => '30.53',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G20330' => array(
			'gene_id' => 'PI00G20330',
			'e_value' => '2e-11',
			'bit_score' => '65.9',
			'alignment_length' => '226',
			'identity_percentage' => '30.53',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC009G03690' => array(
			'gene_id' => 'FC009G03690',
			'e_value' => '5e-11',
			'bit_score' => '66.2',
			'alignment_length' => '214',
			'identity_percentage' => '29.91',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0006G03150' => array(
			'gene_id' => 'AA0006G03150',
			'e_value' => '1e-10',
			'bit_score' => '65.1',
			'alignment_length' => '221',
			'identity_percentage' => '28.51',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh493700' => array(
			'gene_id' => 'emh493700',
			'e_value' => '4e-10',
			'bit_score' => '63.9',
			'alignment_length' => '187',
			'identity_percentage' => '29.95',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_01G02070' => array(
			'gene_id' => 'PTI_01G02070',
			'e_value' => '1e-08',
			'bit_score' => '58.9',
			'alignment_length' => '215',
			'identity_percentage' => '26.51',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_314G00010' => array(
			'gene_id' => 'CNC64A_314G00010',
			'e_value' => '3e-06',
			'bit_score' => '49.7',
			'alignment_length' => '155',
			'identity_percentage' => '29.03',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'emh' => array(
			(int) 0 => 'emh706320',
			(int) 1 => 'emh197970',
			(int) 2 => 'emh584420',
			(int) 3 => 'emh134760',
			(int) 4 => 'emh316230',
			(int) 5 => 'emh292560',
			(int) 6 => 'emh543440',
			(int) 7 => 'emh469180',
			(int) 8 => 'emh493700'
		),
		'ptri' => array(
			(int) 0 => 'PTI_13G02030',
			(int) 1 => 'PTI_04G01420',
			(int) 2 => 'PTI_01G02070'
		),
		'tps' => array(
			(int) 0 => 'TP10G00800',
			(int) 1 => 'TP02G09850',
			(int) 2 => 'TP03G07790'
		),
		'fcy' => array(
			(int) 0 => 'FC003G02470',
			(int) 1 => 'FC002G00620',
			(int) 2 => 'FC009G03690'
		),
		'aan' => array(
			(int) 0 => 'AA0004G02790',
			(int) 1 => 'AA0006G03150'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.02g05280'
		),
		'pse3' => array(
			(int) 0 => 'PI00G20330'
		)
	),
	'gene_id' => 'emh706320',
	'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' => 'emh706320',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'AT5G40155',
	'gf_placeholder' => 'HOM03P009760',
	'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(
	'emh706320' => array(
		'gene_id' => 'emh706320',
		'e_value' => '0.0',
		'bit_score' => '538',
		'alignment_length' => '268',
		'identity_percentage' => '100.00',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'emh197970' => array(
		'gene_id' => 'emh197970',
		'e_value' => '1e-128',
		'bit_score' => '373',
		'alignment_length' => '250',
		'identity_percentage' => '80.80',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'PTI_13G02030' => array(
		'gene_id' => 'PTI_13G02030',
		'e_value' => '1e-70',
		'bit_score' => '225',
		'alignment_length' => '219',
		'identity_percentage' => '58.45',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'TP10G00800' => array(
		'gene_id' => 'TP10G00800',
		'e_value' => '5e-56',
		'bit_score' => '188',
		'alignment_length' => '220',
		'identity_percentage' => '48.18',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'FC003G02470' => array(
		'gene_id' => 'FC003G02470',
		'e_value' => '4e-46',
		'bit_score' => '160',
		'alignment_length' => '220',
		'identity_percentage' => '43.64',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'emh584420' => array(
		'gene_id' => 'emh584420',
		'e_value' => '3e-29',
		'bit_score' => '115',
		'alignment_length' => '228',
		'identity_percentage' => '36.84',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P163236'
		)
	),
	'FC002G00620' => array(
		'gene_id' => 'FC002G00620',
		'e_value' => '4e-26',
		'bit_score' => '108',
		'alignment_length' => '217',
		'identity_percentage' => '32.26',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P039711'
		)
	),
	'PTI_04G01420' => array(
		'gene_id' => 'PTI_04G01420',
		'e_value' => '5e-24',
		'bit_score' => '102',
		'alignment_length' => '224',
		'identity_percentage' => '33.48',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P039711'
		)
	),
	'emh134760' => array(
		'gene_id' => 'emh134760',
		'e_value' => '1e-20',
		'bit_score' => '92.8',
		'alignment_length' => '233',
		'identity_percentage' => '30.90',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P005263'
		)
	),
	'TP02G09850' => array(
		'gene_id' => 'TP02G09850',
		'e_value' => '3e-19',
		'bit_score' => '92.4',
		'alignment_length' => '217',
		'identity_percentage' => '31.34',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P039711'
		)
	),
	'AA0004G02790' => array(
		'gene_id' => 'AA0004G02790',
		'e_value' => '2e-15',
		'bit_score' => '76.3',
		'alignment_length' => '221',
		'identity_percentage' => '28.96',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P155552'
		)
	),
	'TP03G07790' => array(
		'gene_id' => 'TP03G07790',
		'e_value' => '9e-15',
		'bit_score' => '78.2',
		'alignment_length' => '222',
		'identity_percentage' => '30.18',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'emh316230' => array(
		'gene_id' => 'emh316230',
		'e_value' => '2e-13',
		'bit_score' => '73.6',
		'alignment_length' => '225',
		'identity_percentage' => '28.44',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'emh292560' => array(
		'gene_id' => 'emh292560',
		'e_value' => '6e-13',
		'bit_score' => '70.5',
		'alignment_length' => '165',
		'identity_percentage' => '33.33',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P050218'
		)
	),
	'emh543440' => array(
		'gene_id' => 'emh543440',
		'e_value' => '6e-13',
		'bit_score' => '70.5',
		'alignment_length' => '165',
		'identity_percentage' => '33.33',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P050218'
		)
	),
	'emh469180' => array(
		'gene_id' => 'emh469180',
		'e_value' => '5e-12',
		'bit_score' => '67.0',
		'alignment_length' => '216',
		'identity_percentage' => '29.63',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P009816'
		)
	),
	'RCC4223.02g05280' => array(
		'gene_id' => 'RCC4223.02g05280',
		'e_value' => '5e-12',
		'bit_score' => '67.4',
		'alignment_length' => '226',
		'identity_percentage' => '30.53',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'PI00G20330' => array(
		'gene_id' => 'PI00G20330',
		'e_value' => '2e-11',
		'bit_score' => '65.9',
		'alignment_length' => '226',
		'identity_percentage' => '30.53',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'FC009G03690' => array(
		'gene_id' => 'FC009G03690',
		'e_value' => '5e-11',
		'bit_score' => '66.2',
		'alignment_length' => '214',
		'identity_percentage' => '29.91',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'AA0006G03150' => array(
		'gene_id' => 'AA0006G03150',
		'e_value' => '1e-10',
		'bit_score' => '65.1',
		'alignment_length' => '221',
		'identity_percentage' => '28.51',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'emh493700' => array(
		'gene_id' => 'emh493700',
		'e_value' => '4e-10',
		'bit_score' => '63.9',
		'alignment_length' => '187',
		'identity_percentage' => '29.95',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P013114',
			'ORTHOFAM' => 'ORTHO03P005263'
		)
	),
	'PTI_01G02070' => array(
		'gene_id' => 'PTI_01G02070',
		'e_value' => '1e-08',
		'bit_score' => '58.9',
		'alignment_length' => '215',
		'identity_percentage' => '26.51',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'CNC64A_314G00010' => array(
		'gene_id' => 'CNC64A_314G00010',
		'e_value' => '3e-06',
		'bit_score' => '49.7',
		'alignment_length' => '155',
		'identity_percentage' => '29.03',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	)
)
$similarity_hits_species = array(
	'emh' => array(
		(int) 0 => 'emh706320',
		(int) 1 => 'emh197970',
		(int) 2 => 'emh584420',
		(int) 3 => 'emh134760',
		(int) 4 => 'emh316230',
		(int) 5 => 'emh292560',
		(int) 6 => 'emh543440',
		(int) 7 => 'emh469180',
		(int) 8 => 'emh493700'
	),
	'ptri' => array(
		(int) 0 => 'PTI_13G02030',
		(int) 1 => 'PTI_04G01420',
		(int) 2 => 'PTI_01G02070'
	),
	'tps' => array(
		(int) 0 => 'TP10G00800',
		(int) 1 => 'TP02G09850',
		(int) 2 => 'TP03G07790'
	),
	'fcy' => array(
		(int) 0 => 'FC003G02470',
		(int) 1 => 'FC002G00620',
		(int) 2 => 'FC009G03690'
	),
	'aan' => array(
		(int) 0 => 'AA0004G02790',
		(int) 1 => 'AA0006G03150'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.02g05280'
	),
	'pse3' => array(
		(int) 0 => 'PI00G20330'
	)
)
$gene_id = 'emh706320'
$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 = 'emh706320'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'AT5G40155'
$gf_placeholder = 'HOM03P009760'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_314G00010',
	'e_value' => '3e-06',
	'bit_score' => '49.7',
	'alignment_length' => '155',
	'identity_percentage' => '29.03',
	'gf' => array(
		'HOMFAM' => 'HOM03P002238',
		'ORTHOFAM' => 'ORTHO03P007903'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_314G00010'
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(
		'emh706320' => array(
			'gene_id' => 'emh706320',
			'e_value' => '0.0',
			'bit_score' => '538',
			'alignment_length' => '268',
			'identity_percentage' => '100.00',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh197970' => array(
			'gene_id' => 'emh197970',
			'e_value' => '1e-128',
			'bit_score' => '373',
			'alignment_length' => '250',
			'identity_percentage' => '80.80',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_13G02030' => array(
			'gene_id' => 'PTI_13G02030',
			'e_value' => '1e-70',
			'bit_score' => '225',
			'alignment_length' => '219',
			'identity_percentage' => '58.45',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP10G00800' => array(
			'gene_id' => 'TP10G00800',
			'e_value' => '5e-56',
			'bit_score' => '188',
			'alignment_length' => '220',
			'identity_percentage' => '48.18',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC003G02470' => array(
			'gene_id' => 'FC003G02470',
			'e_value' => '4e-46',
			'bit_score' => '160',
			'alignment_length' => '220',
			'identity_percentage' => '43.64',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh584420' => array(
			'gene_id' => 'emh584420',
			'e_value' => '3e-29',
			'bit_score' => '115',
			'alignment_length' => '228',
			'identity_percentage' => '36.84',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC002G00620' => array(
			'gene_id' => 'FC002G00620',
			'e_value' => '4e-26',
			'bit_score' => '108',
			'alignment_length' => '217',
			'identity_percentage' => '32.26',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_04G01420' => array(
			'gene_id' => 'PTI_04G01420',
			'e_value' => '5e-24',
			'bit_score' => '102',
			'alignment_length' => '224',
			'identity_percentage' => '33.48',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh134760' => array(
			'gene_id' => 'emh134760',
			'e_value' => '1e-20',
			'bit_score' => '92.8',
			'alignment_length' => '233',
			'identity_percentage' => '30.90',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP02G09850' => array(
			'gene_id' => 'TP02G09850',
			'e_value' => '3e-19',
			'bit_score' => '92.4',
			'alignment_length' => '217',
			'identity_percentage' => '31.34',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0004G02790' => array(
			'gene_id' => 'AA0004G02790',
			'e_value' => '2e-15',
			'bit_score' => '76.3',
			'alignment_length' => '221',
			'identity_percentage' => '28.96',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP03G07790' => array(
			'gene_id' => 'TP03G07790',
			'e_value' => '9e-15',
			'bit_score' => '78.2',
			'alignment_length' => '222',
			'identity_percentage' => '30.18',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh316230' => array(
			'gene_id' => 'emh316230',
			'e_value' => '2e-13',
			'bit_score' => '73.6',
			'alignment_length' => '225',
			'identity_percentage' => '28.44',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh292560' => array(
			'gene_id' => 'emh292560',
			'e_value' => '6e-13',
			'bit_score' => '70.5',
			'alignment_length' => '165',
			'identity_percentage' => '33.33',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh543440' => array(
			'gene_id' => 'emh543440',
			'e_value' => '6e-13',
			'bit_score' => '70.5',
			'alignment_length' => '165',
			'identity_percentage' => '33.33',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh469180' => array(
			'gene_id' => 'emh469180',
			'e_value' => '5e-12',
			'bit_score' => '67.0',
			'alignment_length' => '216',
			'identity_percentage' => '29.63',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.02g05280' => array(
			'gene_id' => 'RCC4223.02g05280',
			'e_value' => '5e-12',
			'bit_score' => '67.4',
			'alignment_length' => '226',
			'identity_percentage' => '30.53',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G20330' => array(
			'gene_id' => 'PI00G20330',
			'e_value' => '2e-11',
			'bit_score' => '65.9',
			'alignment_length' => '226',
			'identity_percentage' => '30.53',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FC009G03690' => array(
			'gene_id' => 'FC009G03690',
			'e_value' => '5e-11',
			'bit_score' => '66.2',
			'alignment_length' => '214',
			'identity_percentage' => '29.91',
			'species' => 'fcy',
			'common_name' => 'Fragilariopsis cylindrus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0006G03150' => array(
			'gene_id' => 'AA0006G03150',
			'e_value' => '1e-10',
			'bit_score' => '65.1',
			'alignment_length' => '221',
			'identity_percentage' => '28.51',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'emh493700' => array(
			'gene_id' => 'emh493700',
			'e_value' => '4e-10',
			'bit_score' => '63.9',
			'alignment_length' => '187',
			'identity_percentage' => '29.95',
			'species' => 'emh',
			'common_name' => 'Emiliania huxleyi',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_01G02070' => array(
			'gene_id' => 'PTI_01G02070',
			'e_value' => '1e-08',
			'bit_score' => '58.9',
			'alignment_length' => '215',
			'identity_percentage' => '26.51',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_314G00010' => array(
			'gene_id' => 'CNC64A_314G00010',
			'e_value' => '3e-06',
			'bit_score' => '49.7',
			'alignment_length' => '155',
			'identity_percentage' => '29.03',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'emh' => array(
			(int) 0 => 'emh706320',
			(int) 1 => 'emh197970',
			(int) 2 => 'emh584420',
			(int) 3 => 'emh134760',
			(int) 4 => 'emh316230',
			(int) 5 => 'emh292560',
			(int) 6 => 'emh543440',
			(int) 7 => 'emh469180',
			(int) 8 => 'emh493700'
		),
		'ptri' => array(
			(int) 0 => 'PTI_13G02030',
			(int) 1 => 'PTI_04G01420',
			(int) 2 => 'PTI_01G02070'
		),
		'tps' => array(
			(int) 0 => 'TP10G00800',
			(int) 1 => 'TP02G09850',
			(int) 2 => 'TP03G07790'
		),
		'fcy' => array(
			(int) 0 => 'FC003G02470',
			(int) 1 => 'FC002G00620',
			(int) 2 => 'FC009G03690'
		),
		'aan' => array(
			(int) 0 => 'AA0004G02790',
			(int) 1 => 'AA0006G03150'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.02g05280'
		),
		'pse3' => array(
			(int) 0 => 'PI00G20330'
		)
	),
	'gene_id' => 'emh706320',
	'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' => 'emh706320',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'AT5G40155',
	'gf_placeholder' => 'HOM03P009760',
	'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(
	'emh706320' => array(
		'gene_id' => 'emh706320',
		'e_value' => '0.0',
		'bit_score' => '538',
		'alignment_length' => '268',
		'identity_percentage' => '100.00',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'emh197970' => array(
		'gene_id' => 'emh197970',
		'e_value' => '1e-128',
		'bit_score' => '373',
		'alignment_length' => '250',
		'identity_percentage' => '80.80',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'PTI_13G02030' => array(
		'gene_id' => 'PTI_13G02030',
		'e_value' => '1e-70',
		'bit_score' => '225',
		'alignment_length' => '219',
		'identity_percentage' => '58.45',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'TP10G00800' => array(
		'gene_id' => 'TP10G00800',
		'e_value' => '5e-56',
		'bit_score' => '188',
		'alignment_length' => '220',
		'identity_percentage' => '48.18',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'FC003G02470' => array(
		'gene_id' => 'FC003G02470',
		'e_value' => '4e-46',
		'bit_score' => '160',
		'alignment_length' => '220',
		'identity_percentage' => '43.64',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P018367'
		)
	),
	'emh584420' => array(
		'gene_id' => 'emh584420',
		'e_value' => '3e-29',
		'bit_score' => '115',
		'alignment_length' => '228',
		'identity_percentage' => '36.84',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P163236'
		)
	),
	'FC002G00620' => array(
		'gene_id' => 'FC002G00620',
		'e_value' => '4e-26',
		'bit_score' => '108',
		'alignment_length' => '217',
		'identity_percentage' => '32.26',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P039711'
		)
	),
	'PTI_04G01420' => array(
		'gene_id' => 'PTI_04G01420',
		'e_value' => '5e-24',
		'bit_score' => '102',
		'alignment_length' => '224',
		'identity_percentage' => '33.48',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P039711'
		)
	),
	'emh134760' => array(
		'gene_id' => 'emh134760',
		'e_value' => '1e-20',
		'bit_score' => '92.8',
		'alignment_length' => '233',
		'identity_percentage' => '30.90',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P005263'
		)
	),
	'TP02G09850' => array(
		'gene_id' => 'TP02G09850',
		'e_value' => '3e-19',
		'bit_score' => '92.4',
		'alignment_length' => '217',
		'identity_percentage' => '31.34',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P039711'
		)
	),
	'AA0004G02790' => array(
		'gene_id' => 'AA0004G02790',
		'e_value' => '2e-15',
		'bit_score' => '76.3',
		'alignment_length' => '221',
		'identity_percentage' => '28.96',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P155552'
		)
	),
	'TP03G07790' => array(
		'gene_id' => 'TP03G07790',
		'e_value' => '9e-15',
		'bit_score' => '78.2',
		'alignment_length' => '222',
		'identity_percentage' => '30.18',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'emh316230' => array(
		'gene_id' => 'emh316230',
		'e_value' => '2e-13',
		'bit_score' => '73.6',
		'alignment_length' => '225',
		'identity_percentage' => '28.44',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'emh292560' => array(
		'gene_id' => 'emh292560',
		'e_value' => '6e-13',
		'bit_score' => '70.5',
		'alignment_length' => '165',
		'identity_percentage' => '33.33',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P050218'
		)
	),
	'emh543440' => array(
		'gene_id' => 'emh543440',
		'e_value' => '6e-13',
		'bit_score' => '70.5',
		'alignment_length' => '165',
		'identity_percentage' => '33.33',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P050218'
		)
	),
	'emh469180' => array(
		'gene_id' => 'emh469180',
		'e_value' => '5e-12',
		'bit_score' => '67.0',
		'alignment_length' => '216',
		'identity_percentage' => '29.63',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P009816'
		)
	),
	'RCC4223.02g05280' => array(
		'gene_id' => 'RCC4223.02g05280',
		'e_value' => '5e-12',
		'bit_score' => '67.4',
		'alignment_length' => '226',
		'identity_percentage' => '30.53',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'PI00G20330' => array(
		'gene_id' => 'PI00G20330',
		'e_value' => '2e-11',
		'bit_score' => '65.9',
		'alignment_length' => '226',
		'identity_percentage' => '30.53',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'FC009G03690' => array(
		'gene_id' => 'FC009G03690',
		'e_value' => '5e-11',
		'bit_score' => '66.2',
		'alignment_length' => '214',
		'identity_percentage' => '29.91',
		'species' => 'fcy',
		'common_name' => 'Fragilariopsis cylindrus',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'AA0006G03150' => array(
		'gene_id' => 'AA0006G03150',
		'e_value' => '1e-10',
		'bit_score' => '65.1',
		'alignment_length' => '221',
		'identity_percentage' => '28.51',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'emh493700' => array(
		'gene_id' => 'emh493700',
		'e_value' => '4e-10',
		'bit_score' => '63.9',
		'alignment_length' => '187',
		'identity_percentage' => '29.95',
		'species' => 'emh',
		'common_name' => 'Emiliania huxleyi',
		'gf' => array(
			'HOMFAM' => 'HOM03P013114',
			'ORTHOFAM' => 'ORTHO03P005263'
		)
	),
	'PTI_01G02070' => array(
		'gene_id' => 'PTI_01G02070',
		'e_value' => '1e-08',
		'bit_score' => '58.9',
		'alignment_length' => '215',
		'identity_percentage' => '26.51',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	),
	'CNC64A_314G00010' => array(
		'gene_id' => 'CNC64A_314G00010',
		'e_value' => '3e-06',
		'bit_score' => '49.7',
		'alignment_length' => '155',
		'identity_percentage' => '29.03',
		'gf' => array(
			'HOMFAM' => 'HOM03P002238',
			'ORTHOFAM' => 'ORTHO03P007903'
		)
	)
)
$similarity_hits_species = array(
	'emh' => array(
		(int) 0 => 'emh706320',
		(int) 1 => 'emh197970',
		(int) 2 => 'emh584420',
		(int) 3 => 'emh134760',
		(int) 4 => 'emh316230',
		(int) 5 => 'emh292560',
		(int) 6 => 'emh543440',
		(int) 7 => 'emh469180',
		(int) 8 => 'emh493700'
	),
	'ptri' => array(
		(int) 0 => 'PTI_13G02030',
		(int) 1 => 'PTI_04G01420',
		(int) 2 => 'PTI_01G02070'
	),
	'tps' => array(
		(int) 0 => 'TP10G00800',
		(int) 1 => 'TP02G09850',
		(int) 2 => 'TP03G07790'
	),
	'fcy' => array(
		(int) 0 => 'FC003G02470',
		(int) 1 => 'FC002G00620',
		(int) 2 => 'FC009G03690'
	),
	'aan' => array(
		(int) 0 => 'AA0004G02790',
		(int) 1 => 'AA0006G03150'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.02g05280'
	),
	'pse3' => array(
		(int) 0 => 'PI00G20330'
	)
)
$gene_id = 'emh706320'
$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 = 'emh706320'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'AT5G40155'
$gf_placeholder = 'HOM03P009760'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_314G00010',
	'e_value' => '3e-06',
	'bit_score' => '49.7',
	'alignment_length' => '155',
	'identity_percentage' => '29.03',
	'gf' => array(
		'HOMFAM' => 'HOM03P002238',
		'ORTHOFAM' => 'ORTHO03P007903'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_314G00010'
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
emh706320	Emiliania huxleyi	0.0	538	268	100.00
emh197970	Emiliania huxleyi	1e-128	373	250	80.80
PTI_13G02030	Phaeodactylum tricornutum	1e-70	225	219	58.45
TP10G00800	Thalassiosira pseudonana	5e-56	188	220	48.18
FC003G02470	Fragilariopsis cylindrus	4e-46	160	220	43.64
emh584420	Emiliania huxleyi	3e-29	115	228	36.84
FC002G00620	Fragilariopsis cylindrus	4e-26	108	217	32.26
PTI_04G01420	Phaeodactylum tricornutum	5e-24	102	224	33.48
emh134760	Emiliania huxleyi	1e-20	92.8	233	30.90
TP02G09850	Thalassiosira pseudonana	3e-19	92.4	217	31.34
AA0004G02790	Aureococcus anophagefferens	2e-15	76.3	221	28.96
TP03G07790	Thalassiosira pseudonana	9e-15	78.2	222	30.18
emh316230	Emiliania huxleyi	2e-13	73.6	225	28.44
emh292560	Emiliania huxleyi	6e-13	70.5	165	33.33
emh543440	Emiliania huxleyi	6e-13	70.5	165	33.33
emh469180	Emiliania huxleyi	5e-12	67.0	216	29.63
RCC4223.02g05280	Picochlorum_RCC4223	5e-12	67.4	226	30.53
PI00G20330	Picochlorum sp. SENEW3 (SE3)	2e-11	65.9	226	30.53
FC009G03690	Fragilariopsis cylindrus	5e-11	66.2	214	29.91
AA0006G03150	Aureococcus anophagefferens	1e-10	65.1	221	28.51
emh493700	Emiliania huxleyi	4e-10	63.9	187	29.95
PTI_01G02070	Phaeodactylum tricornutum	1e-08	58.9	215	26.51
CNC64A_314G00010		3e-06	49.7	155	29.03

External Sequences (optional)

External Sequences Type

Program Settings

MSA algorithm
Tree construction algorithm
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