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(
		'AT3G13870' => array(
			'gene_id' => 'AT3G13870',
			'e_value' => '0.0',
			'bit_score' => '1655',
			'alignment_length' => '803',
			'identity_percentage' => '100.00',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G72960' => array(
			'gene_id' => 'AT1G72960',
			'e_value' => '0.0',
			'bit_score' => '1251',
			'alignment_length' => '760',
			'identity_percentage' => '78.29',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS01G39310' => array(
			'gene_id' => 'OS01G39310',
			'e_value' => '0.0',
			'bit_score' => '1177',
			'alignment_length' => '784',
			'identity_percentage' => '70.92',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00064G00790' => array(
			'gene_id' => 'ATR_00064G00790',
			'e_value' => '0.0',
			'bit_score' => '1148',
			'alignment_length' => '761',
			'identity_percentage' => '71.35',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00019G03700' => array(
			'gene_id' => 'ATR_00019G03700',
			'e_value' => '0.0',
			'bit_score' => '1144',
			'alignment_length' => '774',
			'identity_percentage' => '70.80',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00002G06160' => array(
			'gene_id' => 'ATR_00002G06160',
			'e_value' => '0.0',
			'bit_score' => '1120',
			'alignment_length' => '782',
			'identity_percentage' => '68.41',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT5G45160' => array(
			'gene_id' => 'AT5G45160',
			'e_value' => '0.0',
			'bit_score' => '1080',
			'alignment_length' => '810',
			'identity_percentage' => '64.57',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS12G41170' => array(
			'gene_id' => 'OS12G41170',
			'e_value' => '0.0',
			'bit_score' => '1046',
			'alignment_length' => '754',
			'identity_percentage' => '64.85',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS11G37260' => array(
			'gene_id' => 'OS11G37260',
			'e_value' => '0.0',
			'bit_score' => '951',
			'alignment_length' => '746',
			'identity_percentage' => '60.59',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00382G00080' => array(
			'gene_id' => 'PP00382G00080',
			'e_value' => '0.0',
			'bit_score' => '948',
			'alignment_length' => '793',
			'identity_percentage' => '57.88',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00132G00620' => array(
			'gene_id' => 'PP00132G00620',
			'e_value' => '0.0',
			'bit_score' => '918',
			'alignment_length' => '773',
			'identity_percentage' => '56.79',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00033G01040' => array(
			'gene_id' => 'PP00033G01040',
			'e_value' => '0.0',
			'bit_score' => '894',
			'alignment_length' => '776',
			'identity_percentage' => '55.28',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G45150' => array(
			'gene_id' => 'CV00G45150',
			'e_value' => '0.0',
			'bit_score' => '588',
			'alignment_length' => '773',
			'identity_percentage' => '40.88',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.11g01590' => array(
			'gene_id' => 'RCC4223.11g01590',
			'e_value' => '0.0',
			'bit_score' => '579',
			'alignment_length' => '787',
			'identity_percentage' => '39.26',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G12780' => array(
			'gene_id' => 'PI00G12780',
			'e_value' => '0.0',
			'bit_score' => '574',
			'alignment_length' => '768',
			'identity_percentage' => '39.71',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G21920' => array(
			'gene_id' => 'VC00G21920',
			'e_value' => '0.0',
			'bit_score' => '562',
			'alignment_length' => '758',
			'identity_percentage' => '40.90',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G64910' => array(
			'gene_id' => 'AC00G64910',
			'e_value' => '0.0',
			'bit_score' => '560',
			'alignment_length' => '761',
			'identity_percentage' => '40.34',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR10G04770' => array(
			'gene_id' => 'CR10G04770',
			'e_value' => '2e-173',
			'bit_score' => '530',
			'alignment_length' => '798',
			'identity_percentage' => '39.85',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OM_02G00590' => array(
			'gene_id' => 'OM_02G00590',
			'e_value' => '2e-166',
			'bit_score' => '510',
			'alignment_length' => '790',
			'identity_percentage' => '35.32',
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL04G00500' => array(
			'gene_id' => 'OL04G00500',
			'e_value' => '4e-166',
			'bit_score' => '509',
			'alignment_length' => '750',
			'identity_percentage' => '37.60',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OT_04G00540' => array(
			'gene_id' => 'OT_04G00540',
			'e_value' => '1e-164',
			'bit_score' => '506',
			'alignment_length' => '816',
			'identity_percentage' => '35.78',
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MRCC299_09G06070' => array(
			'gene_id' => 'MRCC299_09G06070',
			'e_value' => '2e-163',
			'bit_score' => '501',
			'alignment_length' => '758',
			'identity_percentage' => '37.99',
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ORCC809_04G04660' => array(
			'gene_id' => 'ORCC809_04G04660',
			'e_value' => '2e-158',
			'bit_score' => '490',
			'alignment_length' => '758',
			'identity_percentage' => '35.49',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00227G00230' => array(
			'gene_id' => 'PP00227G00230',
			'e_value' => '1e-149',
			'bit_score' => '454',
			'alignment_length' => '488',
			'identity_percentage' => '44.47',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'BPRRCC1105_18G00790' => array(
			'gene_id' => 'BPRRCC1105_18G00790',
			'e_value' => '1e-123',
			'bit_score' => '401',
			'alignment_length' => '862',
			'identity_percentage' => '31.21',
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MP18G00260' => array(
			'gene_id' => 'MP18G00260',
			'e_value' => '2e-120',
			'bit_score' => '393',
			'alignment_length' => '575',
			'identity_percentage' => '38.96',
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G56970' => array(
			'gene_id' => 'AP00G56970',
			'e_value' => '1e-102',
			'bit_score' => '326',
			'alignment_length' => '331',
			'identity_percentage' => '50.15',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'HE0000G07250' => array(
			'gene_id' => 'HE0000G07250',
			'e_value' => '2e-101',
			'bit_score' => '324',
			'alignment_length' => '314',
			'identity_percentage' => '49.68',
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0279823' => array(
			'gene_id' => 'DDB_G0279823',
			'e_value' => '1e-95',
			'bit_score' => '324',
			'alignment_length' => '703',
			'identity_percentage' => '31.72',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YOR165W' => array(
			'gene_id' => 'YOR165W',
			'e_value' => '8e-82',
			'bit_score' => '284',
			'alignment_length' => '741',
			'identity_percentage' => '28.74',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu43150' => array(
			'gene_id' => 'gsu43150',
			'e_value' => '1e-80',
			'bit_score' => '282',
			'alignment_length' => '824',
			'identity_percentage' => '28.16',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr166320' => array(
			'gene_id' => 'ccr166320',
			'e_value' => '1e-79',
			'bit_score' => '279',
			'alignment_length' => '782',
			'identity_percentage' => '29.54',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'SPAC222.14c' => array(
			'gene_id' => 'SPAC222.14c',
			'e_value' => '7e-79',
			'bit_score' => '276',
			'alignment_length' => '724',
			'identity_percentage' => '28.04',
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM14G01410' => array(
			'gene_id' => 'CM14G01410',
			'e_value' => '7e-66',
			'bit_score' => '239',
			'alignment_length' => '290',
			'identity_percentage' => '45.86',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr134780' => array(
			'gene_id' => 'ccr134780',
			'e_value' => '6e-52',
			'bit_score' => '195',
			'alignment_length' => '438',
			'identity_percentage' => '31.74',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte204310' => array(
			'gene_id' => 'pte204310',
			'e_value' => '1e-51',
			'bit_score' => '196',
			'alignment_length' => '712',
			'identity_percentage' => '24.58',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu19480' => array(
			'gene_id' => 'gsu19480',
			'e_value' => '2e-49',
			'bit_score' => '187',
			'alignment_length' => '422',
			'identity_percentage' => '32.46',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu19500' => array(
			'gene_id' => 'gsu19500',
			'e_value' => '1e-48',
			'bit_score' => '184',
			'alignment_length' => '425',
			'identity_percentage' => '32.24',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte340320' => array(
			'gene_id' => 'pte340320',
			'e_value' => '2e-44',
			'bit_score' => '175',
			'alignment_length' => '712',
			'identity_percentage' => '23.74',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_282G00010' => array(
			'gene_id' => 'CNC64A_282G00010',
			'e_value' => '6e-43',
			'bit_score' => '166',
			'alignment_length' => '360',
			'identity_percentage' => '30.28',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr103000' => array(
			'gene_id' => 'ccr103000',
			'e_value' => '9e-38',
			'bit_score' => '153',
			'alignment_length' => '396',
			'identity_percentage' => '31.31',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr153840' => array(
			'gene_id' => 'ccr153840',
			'e_value' => '2e-37',
			'bit_score' => '152',
			'alignment_length' => '387',
			'identity_percentage' => '28.68',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu44220' => array(
			'gene_id' => 'gsu44220',
			'e_value' => '4e-37',
			'bit_score' => '151',
			'alignment_length' => '411',
			'identity_percentage' => '27.49',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu86670' => array(
			'gene_id' => 'gsu86670',
			'e_value' => '1e-35',
			'bit_score' => '147',
			'alignment_length' => '458',
			'identity_percentage' => '27.51',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM17G00540' => array(
			'gene_id' => 'CM17G00540',
			'e_value' => '9e-35',
			'bit_score' => '145',
			'alignment_length' => '500',
			'identity_percentage' => '24.60',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0090G00200' => array(
			'gene_id' => 'ES0090G00200',
			'e_value' => '8e-26',
			'bit_score' => '117',
			'alignment_length' => '383',
			'identity_percentage' => '26.89',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100051g14' => array(
			'gene_id' => 'Naga_100051g14',
			'e_value' => '2e-25',
			'bit_score' => '116',
			'alignment_length' => '393',
			'identity_percentage' => '27.99',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM20G02610' => array(
			'gene_id' => 'CM20G02610',
			'e_value' => '1e-23',
			'bit_score' => '109',
			'alignment_length' => '205',
			'identity_percentage' => '34.15',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0100G00250' => array(
			'gene_id' => 'ES0100G00250',
			'e_value' => '1e-20',
			'bit_score' => '100',
			'alignment_length' => '454',
			'identity_percentage' => '24.01',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu73670' => array(
			'gene_id' => 'gsu73670',
			'e_value' => '8e-17',
			'bit_score' => '88.6',
			'alignment_length' => '376',
			'identity_percentage' => '24.73',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM04G01010' => array(
			'gene_id' => 'CM04G01010',
			'e_value' => '3e-16',
			'bit_score' => '87.0',
			'alignment_length' => '471',
			'identity_percentage' => '22.72',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte547680' => array(
			'gene_id' => 'pte547680',
			'e_value' => '7e-10',
			'bit_score' => '67.0',
			'alignment_length' => '99',
			'identity_percentage' => '36.36',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte537960' => array(
			'gene_id' => 'pte537960',
			'e_value' => '2e-09',
			'bit_score' => '65.5',
			'alignment_length' => '133',
			'identity_percentage' => '33.08',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte142860' => array(
			'gene_id' => 'pte142860',
			'e_value' => '5e-09',
			'bit_score' => '64.3',
			'alignment_length' => '99',
			'identity_percentage' => '41.41',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte702950' => array(
			'gene_id' => 'pte702950',
			'e_value' => '7e-09',
			'bit_score' => '63.9',
			'alignment_length' => '99',
			'identity_percentage' => '36.36',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr123160' => array(
			'gene_id' => 'ccr123160',
			'e_value' => '1e-08',
			'bit_score' => '62.4',
			'alignment_length' => '429',
			'identity_percentage' => '20.75',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte716670' => array(
			'gene_id' => 'pte716670',
			'e_value' => '2e-08',
			'bit_score' => '62.8',
			'alignment_length' => '97',
			'identity_percentage' => '36.08',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte301520' => array(
			'gene_id' => 'pte301520',
			'e_value' => '2e-07',
			'bit_score' => '59.3',
			'alignment_length' => '216',
			'identity_percentage' => '30.09',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte548020' => array(
			'gene_id' => 'pte548020',
			'e_value' => '3e-07',
			'bit_score' => '58.2',
			'alignment_length' => '99',
			'identity_percentage' => '33.33',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte215230' => array(
			'gene_id' => 'pte215230',
			'e_value' => '3e-06',
			'bit_score' => '55.5',
			'alignment_length' => '99',
			'identity_percentage' => '33.33',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte446270' => array(
			'gene_id' => 'pte446270',
			'e_value' => '4e-06',
			'bit_score' => '55.1',
			'alignment_length' => '99',
			'identity_percentage' => '37.37',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'ath' => array(
			(int) 0 => 'AT3G13870',
			(int) 1 => 'AT1G72960',
			(int) 2 => 'AT5G45160'
		),
		'osa' => array(
			(int) 0 => 'OS01G39310',
			(int) 1 => 'OS12G41170',
			(int) 2 => 'OS11G37260'
		),
		'atr' => array(
			(int) 0 => 'ATR_00064G00790',
			(int) 1 => 'ATR_00019G03700',
			(int) 2 => 'ATR_00002G06160'
		),
		'ppa' => array(
			(int) 0 => 'PP00382G00080',
			(int) 1 => 'PP00132G00620',
			(int) 2 => 'PP00033G01040',
			(int) 3 => 'PP00227G00230'
		),
		'cvu' => array(
			(int) 0 => 'CV00G45150'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.11g01590'
		),
		'pse3' => array(
			(int) 0 => 'PI00G12780'
		),
		'vca' => array(
			(int) 0 => 'VC00G21920'
		),
		'acg' => array(
			(int) 0 => 'AC00G64910'
		),
		'cre' => array(
			(int) 0 => 'CR10G04770'
		),
		'ome' => array(
			(int) 0 => 'OM_02G00590'
		),
		'olu' => array(
			(int) 0 => 'OL04G00500'
		),
		'ota' => array(
			(int) 0 => 'OT_04G00540'
		),
		'mrcc299' => array(
			(int) 0 => 'MRCC299_09G06070'
		),
		'orcc809' => array(
			(int) 0 => 'ORCC809_04G04660'
		),
		'bprrcc1105' => array(
			(int) 0 => 'BPRRCC1105_18G00790'
		),
		'mpu' => array(
			(int) 0 => 'MP18G00260'
		),
		'apr' => array(
			(int) 0 => 'AP00G56970'
		),
		'hsp' => array(
			(int) 0 => 'HE0000G07250'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0279823'
		),
		'sac' => array(
			(int) 0 => 'YOR165W'
		),
		'gsu' => array(
			(int) 0 => 'gsu43150',
			(int) 1 => 'gsu19480',
			(int) 2 => 'gsu19500',
			(int) 3 => 'gsu44220',
			(int) 4 => 'gsu86670',
			(int) 5 => 'gsu73670'
		),
		'ccr' => array(
			(int) 0 => 'ccr166320',
			(int) 1 => 'ccr134780',
			(int) 2 => 'ccr103000',
			(int) 3 => 'ccr153840',
			(int) 4 => 'ccr123160'
		),
		'scp' => array(
			(int) 0 => 'SPAC222.14c'
		),
		'cme' => array(
			(int) 0 => 'CM14G01410',
			(int) 1 => 'CM17G00540',
			(int) 2 => 'CM20G02610',
			(int) 3 => 'CM04G01010'
		),
		'pte' => array(
			(int) 0 => 'pte204310',
			(int) 1 => 'pte340320',
			(int) 2 => 'pte547680',
			(int) 3 => 'pte537960',
			(int) 4 => 'pte142860',
			(int) 5 => 'pte702950',
			(int) 6 => 'pte716670',
			(int) 7 => 'pte301520',
			(int) 8 => 'pte548020',
			(int) 9 => 'pte215230',
			(int) 10 => 'pte446270'
		),
		'esi' => array(
			(int) 0 => 'ES0090G00200',
			(int) 1 => 'ES0100G00250'
		),
		'nga' => array(
			(int) 0 => 'Naga_100051g14'
		)
	),
	'gene_id' => 'AT3G13870',
	'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' => 'AT3G13870',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'OM_07G00390',
	'gf_placeholder' => 'HOM03P000971',
	'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(
	'AT3G13870' => array(
		'gene_id' => 'AT3G13870',
		'e_value' => '0.0',
		'bit_score' => '1655',
		'alignment_length' => '803',
		'identity_percentage' => '100.00',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'AT1G72960' => array(
		'gene_id' => 'AT1G72960',
		'e_value' => '0.0',
		'bit_score' => '1251',
		'alignment_length' => '760',
		'identity_percentage' => '78.29',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OS01G39310' => array(
		'gene_id' => 'OS01G39310',
		'e_value' => '0.0',
		'bit_score' => '1177',
		'alignment_length' => '784',
		'identity_percentage' => '70.92',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ATR_00064G00790' => array(
		'gene_id' => 'ATR_00064G00790',
		'e_value' => '0.0',
		'bit_score' => '1148',
		'alignment_length' => '761',
		'identity_percentage' => '71.35',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ATR_00019G03700' => array(
		'gene_id' => 'ATR_00019G03700',
		'e_value' => '0.0',
		'bit_score' => '1144',
		'alignment_length' => '774',
		'identity_percentage' => '70.80',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ATR_00002G06160' => array(
		'gene_id' => 'ATR_00002G06160',
		'e_value' => '0.0',
		'bit_score' => '1120',
		'alignment_length' => '782',
		'identity_percentage' => '68.41',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'AT5G45160' => array(
		'gene_id' => 'AT5G45160',
		'e_value' => '0.0',
		'bit_score' => '1080',
		'alignment_length' => '810',
		'identity_percentage' => '64.57',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OS12G41170' => array(
		'gene_id' => 'OS12G41170',
		'e_value' => '0.0',
		'bit_score' => '1046',
		'alignment_length' => '754',
		'identity_percentage' => '64.85',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OS11G37260' => array(
		'gene_id' => 'OS11G37260',
		'e_value' => '0.0',
		'bit_score' => '951',
		'alignment_length' => '746',
		'identity_percentage' => '60.59',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PP00382G00080' => array(
		'gene_id' => 'PP00382G00080',
		'e_value' => '0.0',
		'bit_score' => '948',
		'alignment_length' => '793',
		'identity_percentage' => '57.88',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PP00132G00620' => array(
		'gene_id' => 'PP00132G00620',
		'e_value' => '0.0',
		'bit_score' => '918',
		'alignment_length' => '773',
		'identity_percentage' => '56.79',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PP00033G01040' => array(
		'gene_id' => 'PP00033G01040',
		'e_value' => '0.0',
		'bit_score' => '894',
		'alignment_length' => '776',
		'identity_percentage' => '55.28',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'CV00G45150' => array(
		'gene_id' => 'CV00G45150',
		'e_value' => '0.0',
		'bit_score' => '588',
		'alignment_length' => '773',
		'identity_percentage' => '40.88',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'RCC4223.11g01590' => array(
		'gene_id' => 'RCC4223.11g01590',
		'e_value' => '0.0',
		'bit_score' => '579',
		'alignment_length' => '787',
		'identity_percentage' => '39.26',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PI00G12780' => array(
		'gene_id' => 'PI00G12780',
		'e_value' => '0.0',
		'bit_score' => '574',
		'alignment_length' => '768',
		'identity_percentage' => '39.71',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'VC00G21920' => array(
		'gene_id' => 'VC00G21920',
		'e_value' => '0.0',
		'bit_score' => '562',
		'alignment_length' => '758',
		'identity_percentage' => '40.90',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'AC00G64910' => array(
		'gene_id' => 'AC00G64910',
		'e_value' => '0.0',
		'bit_score' => '560',
		'alignment_length' => '761',
		'identity_percentage' => '40.34',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'CR10G04770' => array(
		'gene_id' => 'CR10G04770',
		'e_value' => '2e-173',
		'bit_score' => '530',
		'alignment_length' => '798',
		'identity_percentage' => '39.85',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OM_02G00590' => array(
		'gene_id' => 'OM_02G00590',
		'e_value' => '2e-166',
		'bit_score' => '510',
		'alignment_length' => '790',
		'identity_percentage' => '35.32',
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OL04G00500' => array(
		'gene_id' => 'OL04G00500',
		'e_value' => '4e-166',
		'bit_score' => '509',
		'alignment_length' => '750',
		'identity_percentage' => '37.60',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OT_04G00540' => array(
		'gene_id' => 'OT_04G00540',
		'e_value' => '1e-164',
		'bit_score' => '506',
		'alignment_length' => '816',
		'identity_percentage' => '35.78',
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'MRCC299_09G06070' => array(
		'gene_id' => 'MRCC299_09G06070',
		'e_value' => '2e-163',
		'bit_score' => '501',
		'alignment_length' => '758',
		'identity_percentage' => '37.99',
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ORCC809_04G04660' => array(
		'gene_id' => 'ORCC809_04G04660',
		'e_value' => '2e-158',
		'bit_score' => '490',
		'alignment_length' => '758',
		'identity_percentage' => '35.49',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PP00227G00230' => array(
		'gene_id' => 'PP00227G00230',
		'e_value' => '1e-149',
		'bit_score' => '454',
		'alignment_length' => '488',
		'identity_percentage' => '44.47',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'BPRRCC1105_18G00790' => array(
		'gene_id' => 'BPRRCC1105_18G00790',
		'e_value' => '1e-123',
		'bit_score' => '401',
		'alignment_length' => '862',
		'identity_percentage' => '31.21',
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'MP18G00260' => array(
		'gene_id' => 'MP18G00260',
		'e_value' => '2e-120',
		'bit_score' => '393',
		'alignment_length' => '575',
		'identity_percentage' => '38.96',
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'AP00G56970' => array(
		'gene_id' => 'AP00G56970',
		'e_value' => '1e-102',
		'bit_score' => '326',
		'alignment_length' => '331',
		'identity_percentage' => '50.15',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'HE0000G07250' => array(
		'gene_id' => 'HE0000G07250',
		'e_value' => '2e-101',
		'bit_score' => '324',
		'alignment_length' => '314',
		'identity_percentage' => '49.68',
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'DDB_G0279823' => array(
		'gene_id' => 'DDB_G0279823',
		'e_value' => '1e-95',
		'bit_score' => '324',
		'alignment_length' => '703',
		'identity_percentage' => '31.72',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'YOR165W' => array(
		'gene_id' => 'YOR165W',
		'e_value' => '8e-82',
		'bit_score' => '284',
		'alignment_length' => '741',
		'identity_percentage' => '28.74',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'gsu43150' => array(
		'gene_id' => 'gsu43150',
		'e_value' => '1e-80',
		'bit_score' => '282',
		'alignment_length' => '824',
		'identity_percentage' => '28.16',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ccr166320' => array(
		'gene_id' => 'ccr166320',
		'e_value' => '1e-79',
		'bit_score' => '279',
		'alignment_length' => '782',
		'identity_percentage' => '29.54',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'SPAC222.14c' => array(
		'gene_id' => 'SPAC222.14c',
		'e_value' => '7e-79',
		'bit_score' => '276',
		'alignment_length' => '724',
		'identity_percentage' => '28.04',
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'CM14G01410' => array(
		'gene_id' => 'CM14G01410',
		'e_value' => '7e-66',
		'bit_score' => '239',
		'alignment_length' => '290',
		'identity_percentage' => '45.86',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ccr134780' => array(
		'gene_id' => 'ccr134780',
		'e_value' => '6e-52',
		'bit_score' => '195',
		'alignment_length' => '438',
		'identity_percentage' => '31.74',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027778'
		)
	),
	'pte204310' => array(
		'gene_id' => 'pte204310',
		'e_value' => '1e-51',
		'bit_score' => '196',
		'alignment_length' => '712',
		'identity_percentage' => '24.58',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'gsu19480' => array(
		'gene_id' => 'gsu19480',
		'e_value' => '2e-49',
		'bit_score' => '187',
		'alignment_length' => '422',
		'identity_percentage' => '32.46',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P007106'
		)
	),
	'gsu19500' => array(
		'gene_id' => 'gsu19500',
		'e_value' => '1e-48',
		'bit_score' => '184',
		'alignment_length' => '425',
		'identity_percentage' => '32.24',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P007106'
		)
	),
	'pte340320' => array(
		'gene_id' => 'pte340320',
		'e_value' => '2e-44',
		'bit_score' => '175',
		'alignment_length' => '712',
		'identity_percentage' => '23.74',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'CNC64A_282G00010' => array(
		'gene_id' => 'CNC64A_282G00010',
		'e_value' => '6e-43',
		'bit_score' => '166',
		'alignment_length' => '360',
		'identity_percentage' => '30.28',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ccr103000' => array(
		'gene_id' => 'ccr103000',
		'e_value' => '9e-38',
		'bit_score' => '153',
		'alignment_length' => '396',
		'identity_percentage' => '31.31',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P007106'
		)
	),
	'ccr153840' => array(
		'gene_id' => 'ccr153840',
		'e_value' => '2e-37',
		'bit_score' => '152',
		'alignment_length' => '387',
		'identity_percentage' => '28.68',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P007106'
		)
	),
	'gsu44220' => array(
		'gene_id' => 'gsu44220',
		'e_value' => '4e-37',
		'bit_score' => '151',
		'alignment_length' => '411',
		'identity_percentage' => '27.49',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P028710'
		)
	),
	'gsu86670' => array(
		'gene_id' => 'gsu86670',
		'e_value' => '1e-35',
		'bit_score' => '147',
		'alignment_length' => '458',
		'identity_percentage' => '27.51',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027778'
		)
	),
	'CM17G00540' => array(
		'gene_id' => 'CM17G00540',
		'e_value' => '9e-35',
		'bit_score' => '145',
		'alignment_length' => '500',
		'identity_percentage' => '24.60',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P028710'
		)
	),
	'ES0090G00200' => array(
		'gene_id' => 'ES0090G00200',
		'e_value' => '8e-26',
		'bit_score' => '117',
		'alignment_length' => '383',
		'identity_percentage' => '26.89',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P028710'
		)
	),
	'Naga_100051g14' => array(
		'gene_id' => 'Naga_100051g14',
		'e_value' => '2e-25',
		'bit_score' => '116',
		'alignment_length' => '393',
		'identity_percentage' => '27.99',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P028710'
		)
	),
	'CM20G02610' => array(
		'gene_id' => 'CM20G02610',
		'e_value' => '1e-23',
		'bit_score' => '109',
		'alignment_length' => '205',
		'identity_percentage' => '34.15',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027778'
		)
	),
	'ES0100G00250' => array(
		'gene_id' => 'ES0100G00250',
		'e_value' => '1e-20',
		'bit_score' => '100',
		'alignment_length' => '454',
		'identity_percentage' => '24.01',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027778'
		)
	),
	'gsu73670' => array(
		'gene_id' => 'gsu73670',
		'e_value' => '8e-17',
		'bit_score' => '88.6',
		'alignment_length' => '376',
		'identity_percentage' => '24.73',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P063471'
		)
	),
	'CM04G01010' => array(
		'gene_id' => 'CM04G01010',
		'e_value' => '3e-16',
		'bit_score' => '87.0',
		'alignment_length' => '471',
		'identity_percentage' => '22.72',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027252'
		)
	),
	'pte547680' => array(
		'gene_id' => 'pte547680',
		'e_value' => '7e-10',
		'bit_score' => '67.0',
		'alignment_length' => '99',
		'identity_percentage' => '36.36',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P022080'
		)
	),
	'pte537960' => array(
		'gene_id' => 'pte537960',
		'e_value' => '2e-09',
		'bit_score' => '65.5',
		'alignment_length' => '133',
		'identity_percentage' => '33.08',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte142860' => array(
		'gene_id' => 'pte142860',
		'e_value' => '5e-09',
		'bit_score' => '64.3',
		'alignment_length' => '99',
		'identity_percentage' => '41.41',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte702950' => array(
		'gene_id' => 'pte702950',
		'e_value' => '7e-09',
		'bit_score' => '63.9',
		'alignment_length' => '99',
		'identity_percentage' => '36.36',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'ccr123160' => array(
		'gene_id' => 'ccr123160',
		'e_value' => '1e-08',
		'bit_score' => '62.4',
		'alignment_length' => '429',
		'identity_percentage' => '20.75',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P063471'
		)
	),
	'pte716670' => array(
		'gene_id' => 'pte716670',
		'e_value' => '2e-08',
		'bit_score' => '62.8',
		'alignment_length' => '97',
		'identity_percentage' => '36.08',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte301520' => array(
		'gene_id' => 'pte301520',
		'e_value' => '2e-07',
		'bit_score' => '59.3',
		'alignment_length' => '216',
		'identity_percentage' => '30.09',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P010876',
			'ORTHOFAM' => 'ORTHO03P011814'
		)
	),
	'pte548020' => array(
		'gene_id' => 'pte548020',
		'e_value' => '3e-07',
		'bit_score' => '58.2',
		'alignment_length' => '99',
		'identity_percentage' => '33.33',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte215230' => array(
		'gene_id' => 'pte215230',
		'e_value' => '3e-06',
		'bit_score' => '55.5',
		'alignment_length' => '99',
		'identity_percentage' => '33.33',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte446270' => array(
		'gene_id' => 'pte446270',
		'e_value' => '4e-06',
		'bit_score' => '55.1',
		'alignment_length' => '99',
		'identity_percentage' => '37.37',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	)
)
$similarity_hits_species = array(
	'ath' => array(
		(int) 0 => 'AT3G13870',
		(int) 1 => 'AT1G72960',
		(int) 2 => 'AT5G45160'
	),
	'osa' => array(
		(int) 0 => 'OS01G39310',
		(int) 1 => 'OS12G41170',
		(int) 2 => 'OS11G37260'
	),
	'atr' => array(
		(int) 0 => 'ATR_00064G00790',
		(int) 1 => 'ATR_00019G03700',
		(int) 2 => 'ATR_00002G06160'
	),
	'ppa' => array(
		(int) 0 => 'PP00382G00080',
		(int) 1 => 'PP00132G00620',
		(int) 2 => 'PP00033G01040',
		(int) 3 => 'PP00227G00230'
	),
	'cvu' => array(
		(int) 0 => 'CV00G45150'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.11g01590'
	),
	'pse3' => array(
		(int) 0 => 'PI00G12780'
	),
	'vca' => array(
		(int) 0 => 'VC00G21920'
	),
	'acg' => array(
		(int) 0 => 'AC00G64910'
	),
	'cre' => array(
		(int) 0 => 'CR10G04770'
	),
	'ome' => array(
		(int) 0 => 'OM_02G00590'
	),
	'olu' => array(
		(int) 0 => 'OL04G00500'
	),
	'ota' => array(
		(int) 0 => 'OT_04G00540'
	),
	'mrcc299' => array(
		(int) 0 => 'MRCC299_09G06070'
	),
	'orcc809' => array(
		(int) 0 => 'ORCC809_04G04660'
	),
	'bprrcc1105' => array(
		(int) 0 => 'BPRRCC1105_18G00790'
	),
	'mpu' => array(
		(int) 0 => 'MP18G00260'
	),
	'apr' => array(
		(int) 0 => 'AP00G56970'
	),
	'hsp' => array(
		(int) 0 => 'HE0000G07250'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0279823'
	),
	'sac' => array(
		(int) 0 => 'YOR165W'
	),
	'gsu' => array(
		(int) 0 => 'gsu43150',
		(int) 1 => 'gsu19480',
		(int) 2 => 'gsu19500',
		(int) 3 => 'gsu44220',
		(int) 4 => 'gsu86670',
		(int) 5 => 'gsu73670'
	),
	'ccr' => array(
		(int) 0 => 'ccr166320',
		(int) 1 => 'ccr134780',
		(int) 2 => 'ccr103000',
		(int) 3 => 'ccr153840',
		(int) 4 => 'ccr123160'
	),
	'scp' => array(
		(int) 0 => 'SPAC222.14c'
	),
	'cme' => array(
		(int) 0 => 'CM14G01410',
		(int) 1 => 'CM17G00540',
		(int) 2 => 'CM20G02610',
		(int) 3 => 'CM04G01010'
	),
	'pte' => array(
		(int) 0 => 'pte204310',
		(int) 1 => 'pte340320',
		(int) 2 => 'pte547680',
		(int) 3 => 'pte537960',
		(int) 4 => 'pte142860',
		(int) 5 => 'pte702950',
		(int) 6 => 'pte716670',
		(int) 7 => 'pte301520',
		(int) 8 => 'pte548020',
		(int) 9 => 'pte215230',
		(int) 10 => 'pte446270'
	),
	'esi' => array(
		(int) 0 => 'ES0090G00200',
		(int) 1 => 'ES0100G00250'
	),
	'nga' => array(
		(int) 0 => 'Naga_100051g14'
	)
)
$gene_id = 'AT3G13870'
$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 = 'AT3G13870'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'OM_07G00390'
$gf_placeholder = 'HOM03P000971'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_282G00010',
	'e_value' => '6e-43',
	'bit_score' => '166',
	'alignment_length' => '360',
	'identity_percentage' => '30.28',
	'gf' => array(
		'HOMFAM' => 'HOM03P001314',
		'ORTHOFAM' => 'ORTHO03P001532'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_282G00010'
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(
		'AT3G13870' => array(
			'gene_id' => 'AT3G13870',
			'e_value' => '0.0',
			'bit_score' => '1655',
			'alignment_length' => '803',
			'identity_percentage' => '100.00',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G72960' => array(
			'gene_id' => 'AT1G72960',
			'e_value' => '0.0',
			'bit_score' => '1251',
			'alignment_length' => '760',
			'identity_percentage' => '78.29',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS01G39310' => array(
			'gene_id' => 'OS01G39310',
			'e_value' => '0.0',
			'bit_score' => '1177',
			'alignment_length' => '784',
			'identity_percentage' => '70.92',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00064G00790' => array(
			'gene_id' => 'ATR_00064G00790',
			'e_value' => '0.0',
			'bit_score' => '1148',
			'alignment_length' => '761',
			'identity_percentage' => '71.35',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00019G03700' => array(
			'gene_id' => 'ATR_00019G03700',
			'e_value' => '0.0',
			'bit_score' => '1144',
			'alignment_length' => '774',
			'identity_percentage' => '70.80',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00002G06160' => array(
			'gene_id' => 'ATR_00002G06160',
			'e_value' => '0.0',
			'bit_score' => '1120',
			'alignment_length' => '782',
			'identity_percentage' => '68.41',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT5G45160' => array(
			'gene_id' => 'AT5G45160',
			'e_value' => '0.0',
			'bit_score' => '1080',
			'alignment_length' => '810',
			'identity_percentage' => '64.57',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS12G41170' => array(
			'gene_id' => 'OS12G41170',
			'e_value' => '0.0',
			'bit_score' => '1046',
			'alignment_length' => '754',
			'identity_percentage' => '64.85',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS11G37260' => array(
			'gene_id' => 'OS11G37260',
			'e_value' => '0.0',
			'bit_score' => '951',
			'alignment_length' => '746',
			'identity_percentage' => '60.59',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00382G00080' => array(
			'gene_id' => 'PP00382G00080',
			'e_value' => '0.0',
			'bit_score' => '948',
			'alignment_length' => '793',
			'identity_percentage' => '57.88',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00132G00620' => array(
			'gene_id' => 'PP00132G00620',
			'e_value' => '0.0',
			'bit_score' => '918',
			'alignment_length' => '773',
			'identity_percentage' => '56.79',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00033G01040' => array(
			'gene_id' => 'PP00033G01040',
			'e_value' => '0.0',
			'bit_score' => '894',
			'alignment_length' => '776',
			'identity_percentage' => '55.28',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G45150' => array(
			'gene_id' => 'CV00G45150',
			'e_value' => '0.0',
			'bit_score' => '588',
			'alignment_length' => '773',
			'identity_percentage' => '40.88',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'RCC4223.11g01590' => array(
			'gene_id' => 'RCC4223.11g01590',
			'e_value' => '0.0',
			'bit_score' => '579',
			'alignment_length' => '787',
			'identity_percentage' => '39.26',
			'species' => 'prcc4223',
			'common_name' => 'Picochlorum_RCC4223',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PI00G12780' => array(
			'gene_id' => 'PI00G12780',
			'e_value' => '0.0',
			'bit_score' => '574',
			'alignment_length' => '768',
			'identity_percentage' => '39.71',
			'species' => 'pse3',
			'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G21920' => array(
			'gene_id' => 'VC00G21920',
			'e_value' => '0.0',
			'bit_score' => '562',
			'alignment_length' => '758',
			'identity_percentage' => '40.90',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G64910' => array(
			'gene_id' => 'AC00G64910',
			'e_value' => '0.0',
			'bit_score' => '560',
			'alignment_length' => '761',
			'identity_percentage' => '40.34',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR10G04770' => array(
			'gene_id' => 'CR10G04770',
			'e_value' => '2e-173',
			'bit_score' => '530',
			'alignment_length' => '798',
			'identity_percentage' => '39.85',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OM_02G00590' => array(
			'gene_id' => 'OM_02G00590',
			'e_value' => '2e-166',
			'bit_score' => '510',
			'alignment_length' => '790',
			'identity_percentage' => '35.32',
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL04G00500' => array(
			'gene_id' => 'OL04G00500',
			'e_value' => '4e-166',
			'bit_score' => '509',
			'alignment_length' => '750',
			'identity_percentage' => '37.60',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OT_04G00540' => array(
			'gene_id' => 'OT_04G00540',
			'e_value' => '1e-164',
			'bit_score' => '506',
			'alignment_length' => '816',
			'identity_percentage' => '35.78',
			'species' => 'ota',
			'common_name' => 'Ostreococcus tauri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MRCC299_09G06070' => array(
			'gene_id' => 'MRCC299_09G06070',
			'e_value' => '2e-163',
			'bit_score' => '501',
			'alignment_length' => '758',
			'identity_percentage' => '37.99',
			'species' => 'mrcc299',
			'common_name' => 'Micromonas sp RCC299',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ORCC809_04G04660' => array(
			'gene_id' => 'ORCC809_04G04660',
			'e_value' => '2e-158',
			'bit_score' => '490',
			'alignment_length' => '758',
			'identity_percentage' => '35.49',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00227G00230' => array(
			'gene_id' => 'PP00227G00230',
			'e_value' => '1e-149',
			'bit_score' => '454',
			'alignment_length' => '488',
			'identity_percentage' => '44.47',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'BPRRCC1105_18G00790' => array(
			'gene_id' => 'BPRRCC1105_18G00790',
			'e_value' => '1e-123',
			'bit_score' => '401',
			'alignment_length' => '862',
			'identity_percentage' => '31.21',
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MP18G00260' => array(
			'gene_id' => 'MP18G00260',
			'e_value' => '2e-120',
			'bit_score' => '393',
			'alignment_length' => '575',
			'identity_percentage' => '38.96',
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G56970' => array(
			'gene_id' => 'AP00G56970',
			'e_value' => '1e-102',
			'bit_score' => '326',
			'alignment_length' => '331',
			'identity_percentage' => '50.15',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'HE0000G07250' => array(
			'gene_id' => 'HE0000G07250',
			'e_value' => '2e-101',
			'bit_score' => '324',
			'alignment_length' => '314',
			'identity_percentage' => '49.68',
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0279823' => array(
			'gene_id' => 'DDB_G0279823',
			'e_value' => '1e-95',
			'bit_score' => '324',
			'alignment_length' => '703',
			'identity_percentage' => '31.72',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YOR165W' => array(
			'gene_id' => 'YOR165W',
			'e_value' => '8e-82',
			'bit_score' => '284',
			'alignment_length' => '741',
			'identity_percentage' => '28.74',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu43150' => array(
			'gene_id' => 'gsu43150',
			'e_value' => '1e-80',
			'bit_score' => '282',
			'alignment_length' => '824',
			'identity_percentage' => '28.16',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr166320' => array(
			'gene_id' => 'ccr166320',
			'e_value' => '1e-79',
			'bit_score' => '279',
			'alignment_length' => '782',
			'identity_percentage' => '29.54',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'SPAC222.14c' => array(
			'gene_id' => 'SPAC222.14c',
			'e_value' => '7e-79',
			'bit_score' => '276',
			'alignment_length' => '724',
			'identity_percentage' => '28.04',
			'species' => 'scp',
			'common_name' => 'Schizosaccharomyces pombe',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM14G01410' => array(
			'gene_id' => 'CM14G01410',
			'e_value' => '7e-66',
			'bit_score' => '239',
			'alignment_length' => '290',
			'identity_percentage' => '45.86',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr134780' => array(
			'gene_id' => 'ccr134780',
			'e_value' => '6e-52',
			'bit_score' => '195',
			'alignment_length' => '438',
			'identity_percentage' => '31.74',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte204310' => array(
			'gene_id' => 'pte204310',
			'e_value' => '1e-51',
			'bit_score' => '196',
			'alignment_length' => '712',
			'identity_percentage' => '24.58',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu19480' => array(
			'gene_id' => 'gsu19480',
			'e_value' => '2e-49',
			'bit_score' => '187',
			'alignment_length' => '422',
			'identity_percentage' => '32.46',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu19500' => array(
			'gene_id' => 'gsu19500',
			'e_value' => '1e-48',
			'bit_score' => '184',
			'alignment_length' => '425',
			'identity_percentage' => '32.24',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte340320' => array(
			'gene_id' => 'pte340320',
			'e_value' => '2e-44',
			'bit_score' => '175',
			'alignment_length' => '712',
			'identity_percentage' => '23.74',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_282G00010' => array(
			'gene_id' => 'CNC64A_282G00010',
			'e_value' => '6e-43',
			'bit_score' => '166',
			'alignment_length' => '360',
			'identity_percentage' => '30.28',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr103000' => array(
			'gene_id' => 'ccr103000',
			'e_value' => '9e-38',
			'bit_score' => '153',
			'alignment_length' => '396',
			'identity_percentage' => '31.31',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr153840' => array(
			'gene_id' => 'ccr153840',
			'e_value' => '2e-37',
			'bit_score' => '152',
			'alignment_length' => '387',
			'identity_percentage' => '28.68',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu44220' => array(
			'gene_id' => 'gsu44220',
			'e_value' => '4e-37',
			'bit_score' => '151',
			'alignment_length' => '411',
			'identity_percentage' => '27.49',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu86670' => array(
			'gene_id' => 'gsu86670',
			'e_value' => '1e-35',
			'bit_score' => '147',
			'alignment_length' => '458',
			'identity_percentage' => '27.51',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM17G00540' => array(
			'gene_id' => 'CM17G00540',
			'e_value' => '9e-35',
			'bit_score' => '145',
			'alignment_length' => '500',
			'identity_percentage' => '24.60',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0090G00200' => array(
			'gene_id' => 'ES0090G00200',
			'e_value' => '8e-26',
			'bit_score' => '117',
			'alignment_length' => '383',
			'identity_percentage' => '26.89',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100051g14' => array(
			'gene_id' => 'Naga_100051g14',
			'e_value' => '2e-25',
			'bit_score' => '116',
			'alignment_length' => '393',
			'identity_percentage' => '27.99',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM20G02610' => array(
			'gene_id' => 'CM20G02610',
			'e_value' => '1e-23',
			'bit_score' => '109',
			'alignment_length' => '205',
			'identity_percentage' => '34.15',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0100G00250' => array(
			'gene_id' => 'ES0100G00250',
			'e_value' => '1e-20',
			'bit_score' => '100',
			'alignment_length' => '454',
			'identity_percentage' => '24.01',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'gsu73670' => array(
			'gene_id' => 'gsu73670',
			'e_value' => '8e-17',
			'bit_score' => '88.6',
			'alignment_length' => '376',
			'identity_percentage' => '24.73',
			'species' => 'gsu',
			'common_name' => 'Galdieria sulphuraria',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CM04G01010' => array(
			'gene_id' => 'CM04G01010',
			'e_value' => '3e-16',
			'bit_score' => '87.0',
			'alignment_length' => '471',
			'identity_percentage' => '22.72',
			'species' => 'cme',
			'common_name' => 'Cyanidioschyzon merolae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte547680' => array(
			'gene_id' => 'pte547680',
			'e_value' => '7e-10',
			'bit_score' => '67.0',
			'alignment_length' => '99',
			'identity_percentage' => '36.36',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte537960' => array(
			'gene_id' => 'pte537960',
			'e_value' => '2e-09',
			'bit_score' => '65.5',
			'alignment_length' => '133',
			'identity_percentage' => '33.08',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte142860' => array(
			'gene_id' => 'pte142860',
			'e_value' => '5e-09',
			'bit_score' => '64.3',
			'alignment_length' => '99',
			'identity_percentage' => '41.41',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte702950' => array(
			'gene_id' => 'pte702950',
			'e_value' => '7e-09',
			'bit_score' => '63.9',
			'alignment_length' => '99',
			'identity_percentage' => '36.36',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ccr123160' => array(
			'gene_id' => 'ccr123160',
			'e_value' => '1e-08',
			'bit_score' => '62.4',
			'alignment_length' => '429',
			'identity_percentage' => '20.75',
			'species' => 'ccr',
			'common_name' => 'Chondrus crispus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte716670' => array(
			'gene_id' => 'pte716670',
			'e_value' => '2e-08',
			'bit_score' => '62.8',
			'alignment_length' => '97',
			'identity_percentage' => '36.08',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte301520' => array(
			'gene_id' => 'pte301520',
			'e_value' => '2e-07',
			'bit_score' => '59.3',
			'alignment_length' => '216',
			'identity_percentage' => '30.09',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte548020' => array(
			'gene_id' => 'pte548020',
			'e_value' => '3e-07',
			'bit_score' => '58.2',
			'alignment_length' => '99',
			'identity_percentage' => '33.33',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte215230' => array(
			'gene_id' => 'pte215230',
			'e_value' => '3e-06',
			'bit_score' => '55.5',
			'alignment_length' => '99',
			'identity_percentage' => '33.33',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'pte446270' => array(
			'gene_id' => 'pte446270',
			'e_value' => '4e-06',
			'bit_score' => '55.1',
			'alignment_length' => '99',
			'identity_percentage' => '37.37',
			'species' => 'pte',
			'common_name' => 'Paramecium tetraurelia',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'ath' => array(
			(int) 0 => 'AT3G13870',
			(int) 1 => 'AT1G72960',
			(int) 2 => 'AT5G45160'
		),
		'osa' => array(
			(int) 0 => 'OS01G39310',
			(int) 1 => 'OS12G41170',
			(int) 2 => 'OS11G37260'
		),
		'atr' => array(
			(int) 0 => 'ATR_00064G00790',
			(int) 1 => 'ATR_00019G03700',
			(int) 2 => 'ATR_00002G06160'
		),
		'ppa' => array(
			(int) 0 => 'PP00382G00080',
			(int) 1 => 'PP00132G00620',
			(int) 2 => 'PP00033G01040',
			(int) 3 => 'PP00227G00230'
		),
		'cvu' => array(
			(int) 0 => 'CV00G45150'
		),
		'prcc4223' => array(
			(int) 0 => 'RCC4223.11g01590'
		),
		'pse3' => array(
			(int) 0 => 'PI00G12780'
		),
		'vca' => array(
			(int) 0 => 'VC00G21920'
		),
		'acg' => array(
			(int) 0 => 'AC00G64910'
		),
		'cre' => array(
			(int) 0 => 'CR10G04770'
		),
		'ome' => array(
			(int) 0 => 'OM_02G00590'
		),
		'olu' => array(
			(int) 0 => 'OL04G00500'
		),
		'ota' => array(
			(int) 0 => 'OT_04G00540'
		),
		'mrcc299' => array(
			(int) 0 => 'MRCC299_09G06070'
		),
		'orcc809' => array(
			(int) 0 => 'ORCC809_04G04660'
		),
		'bprrcc1105' => array(
			(int) 0 => 'BPRRCC1105_18G00790'
		),
		'mpu' => array(
			(int) 0 => 'MP18G00260'
		),
		'apr' => array(
			(int) 0 => 'AP00G56970'
		),
		'hsp' => array(
			(int) 0 => 'HE0000G07250'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0279823'
		),
		'sac' => array(
			(int) 0 => 'YOR165W'
		),
		'gsu' => array(
			(int) 0 => 'gsu43150',
			(int) 1 => 'gsu19480',
			(int) 2 => 'gsu19500',
			(int) 3 => 'gsu44220',
			(int) 4 => 'gsu86670',
			(int) 5 => 'gsu73670'
		),
		'ccr' => array(
			(int) 0 => 'ccr166320',
			(int) 1 => 'ccr134780',
			(int) 2 => 'ccr103000',
			(int) 3 => 'ccr153840',
			(int) 4 => 'ccr123160'
		),
		'scp' => array(
			(int) 0 => 'SPAC222.14c'
		),
		'cme' => array(
			(int) 0 => 'CM14G01410',
			(int) 1 => 'CM17G00540',
			(int) 2 => 'CM20G02610',
			(int) 3 => 'CM04G01010'
		),
		'pte' => array(
			(int) 0 => 'pte204310',
			(int) 1 => 'pte340320',
			(int) 2 => 'pte547680',
			(int) 3 => 'pte537960',
			(int) 4 => 'pte142860',
			(int) 5 => 'pte702950',
			(int) 6 => 'pte716670',
			(int) 7 => 'pte301520',
			(int) 8 => 'pte548020',
			(int) 9 => 'pte215230',
			(int) 10 => 'pte446270'
		),
		'esi' => array(
			(int) 0 => 'ES0090G00200',
			(int) 1 => 'ES0100G00250'
		),
		'nga' => array(
			(int) 0 => 'Naga_100051g14'
		)
	),
	'gene_id' => 'AT3G13870',
	'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' => 'AT3G13870',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'OM_07G00390',
	'gf_placeholder' => 'HOM03P000971',
	'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(
	'AT3G13870' => array(
		'gene_id' => 'AT3G13870',
		'e_value' => '0.0',
		'bit_score' => '1655',
		'alignment_length' => '803',
		'identity_percentage' => '100.00',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'AT1G72960' => array(
		'gene_id' => 'AT1G72960',
		'e_value' => '0.0',
		'bit_score' => '1251',
		'alignment_length' => '760',
		'identity_percentage' => '78.29',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OS01G39310' => array(
		'gene_id' => 'OS01G39310',
		'e_value' => '0.0',
		'bit_score' => '1177',
		'alignment_length' => '784',
		'identity_percentage' => '70.92',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ATR_00064G00790' => array(
		'gene_id' => 'ATR_00064G00790',
		'e_value' => '0.0',
		'bit_score' => '1148',
		'alignment_length' => '761',
		'identity_percentage' => '71.35',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ATR_00019G03700' => array(
		'gene_id' => 'ATR_00019G03700',
		'e_value' => '0.0',
		'bit_score' => '1144',
		'alignment_length' => '774',
		'identity_percentage' => '70.80',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ATR_00002G06160' => array(
		'gene_id' => 'ATR_00002G06160',
		'e_value' => '0.0',
		'bit_score' => '1120',
		'alignment_length' => '782',
		'identity_percentage' => '68.41',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'AT5G45160' => array(
		'gene_id' => 'AT5G45160',
		'e_value' => '0.0',
		'bit_score' => '1080',
		'alignment_length' => '810',
		'identity_percentage' => '64.57',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OS12G41170' => array(
		'gene_id' => 'OS12G41170',
		'e_value' => '0.0',
		'bit_score' => '1046',
		'alignment_length' => '754',
		'identity_percentage' => '64.85',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OS11G37260' => array(
		'gene_id' => 'OS11G37260',
		'e_value' => '0.0',
		'bit_score' => '951',
		'alignment_length' => '746',
		'identity_percentage' => '60.59',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PP00382G00080' => array(
		'gene_id' => 'PP00382G00080',
		'e_value' => '0.0',
		'bit_score' => '948',
		'alignment_length' => '793',
		'identity_percentage' => '57.88',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PP00132G00620' => array(
		'gene_id' => 'PP00132G00620',
		'e_value' => '0.0',
		'bit_score' => '918',
		'alignment_length' => '773',
		'identity_percentage' => '56.79',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PP00033G01040' => array(
		'gene_id' => 'PP00033G01040',
		'e_value' => '0.0',
		'bit_score' => '894',
		'alignment_length' => '776',
		'identity_percentage' => '55.28',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'CV00G45150' => array(
		'gene_id' => 'CV00G45150',
		'e_value' => '0.0',
		'bit_score' => '588',
		'alignment_length' => '773',
		'identity_percentage' => '40.88',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'RCC4223.11g01590' => array(
		'gene_id' => 'RCC4223.11g01590',
		'e_value' => '0.0',
		'bit_score' => '579',
		'alignment_length' => '787',
		'identity_percentage' => '39.26',
		'species' => 'prcc4223',
		'common_name' => 'Picochlorum_RCC4223',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PI00G12780' => array(
		'gene_id' => 'PI00G12780',
		'e_value' => '0.0',
		'bit_score' => '574',
		'alignment_length' => '768',
		'identity_percentage' => '39.71',
		'species' => 'pse3',
		'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'VC00G21920' => array(
		'gene_id' => 'VC00G21920',
		'e_value' => '0.0',
		'bit_score' => '562',
		'alignment_length' => '758',
		'identity_percentage' => '40.90',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'AC00G64910' => array(
		'gene_id' => 'AC00G64910',
		'e_value' => '0.0',
		'bit_score' => '560',
		'alignment_length' => '761',
		'identity_percentage' => '40.34',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'CR10G04770' => array(
		'gene_id' => 'CR10G04770',
		'e_value' => '2e-173',
		'bit_score' => '530',
		'alignment_length' => '798',
		'identity_percentage' => '39.85',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OM_02G00590' => array(
		'gene_id' => 'OM_02G00590',
		'e_value' => '2e-166',
		'bit_score' => '510',
		'alignment_length' => '790',
		'identity_percentage' => '35.32',
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OL04G00500' => array(
		'gene_id' => 'OL04G00500',
		'e_value' => '4e-166',
		'bit_score' => '509',
		'alignment_length' => '750',
		'identity_percentage' => '37.60',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'OT_04G00540' => array(
		'gene_id' => 'OT_04G00540',
		'e_value' => '1e-164',
		'bit_score' => '506',
		'alignment_length' => '816',
		'identity_percentage' => '35.78',
		'species' => 'ota',
		'common_name' => 'Ostreococcus tauri',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'MRCC299_09G06070' => array(
		'gene_id' => 'MRCC299_09G06070',
		'e_value' => '2e-163',
		'bit_score' => '501',
		'alignment_length' => '758',
		'identity_percentage' => '37.99',
		'species' => 'mrcc299',
		'common_name' => 'Micromonas sp RCC299',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ORCC809_04G04660' => array(
		'gene_id' => 'ORCC809_04G04660',
		'e_value' => '2e-158',
		'bit_score' => '490',
		'alignment_length' => '758',
		'identity_percentage' => '35.49',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'PP00227G00230' => array(
		'gene_id' => 'PP00227G00230',
		'e_value' => '1e-149',
		'bit_score' => '454',
		'alignment_length' => '488',
		'identity_percentage' => '44.47',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'BPRRCC1105_18G00790' => array(
		'gene_id' => 'BPRRCC1105_18G00790',
		'e_value' => '1e-123',
		'bit_score' => '401',
		'alignment_length' => '862',
		'identity_percentage' => '31.21',
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'MP18G00260' => array(
		'gene_id' => 'MP18G00260',
		'e_value' => '2e-120',
		'bit_score' => '393',
		'alignment_length' => '575',
		'identity_percentage' => '38.96',
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'AP00G56970' => array(
		'gene_id' => 'AP00G56970',
		'e_value' => '1e-102',
		'bit_score' => '326',
		'alignment_length' => '331',
		'identity_percentage' => '50.15',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'HE0000G07250' => array(
		'gene_id' => 'HE0000G07250',
		'e_value' => '2e-101',
		'bit_score' => '324',
		'alignment_length' => '314',
		'identity_percentage' => '49.68',
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'DDB_G0279823' => array(
		'gene_id' => 'DDB_G0279823',
		'e_value' => '1e-95',
		'bit_score' => '324',
		'alignment_length' => '703',
		'identity_percentage' => '31.72',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'YOR165W' => array(
		'gene_id' => 'YOR165W',
		'e_value' => '8e-82',
		'bit_score' => '284',
		'alignment_length' => '741',
		'identity_percentage' => '28.74',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'gsu43150' => array(
		'gene_id' => 'gsu43150',
		'e_value' => '1e-80',
		'bit_score' => '282',
		'alignment_length' => '824',
		'identity_percentage' => '28.16',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ccr166320' => array(
		'gene_id' => 'ccr166320',
		'e_value' => '1e-79',
		'bit_score' => '279',
		'alignment_length' => '782',
		'identity_percentage' => '29.54',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'SPAC222.14c' => array(
		'gene_id' => 'SPAC222.14c',
		'e_value' => '7e-79',
		'bit_score' => '276',
		'alignment_length' => '724',
		'identity_percentage' => '28.04',
		'species' => 'scp',
		'common_name' => 'Schizosaccharomyces pombe',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'CM14G01410' => array(
		'gene_id' => 'CM14G01410',
		'e_value' => '7e-66',
		'bit_score' => '239',
		'alignment_length' => '290',
		'identity_percentage' => '45.86',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ccr134780' => array(
		'gene_id' => 'ccr134780',
		'e_value' => '6e-52',
		'bit_score' => '195',
		'alignment_length' => '438',
		'identity_percentage' => '31.74',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027778'
		)
	),
	'pte204310' => array(
		'gene_id' => 'pte204310',
		'e_value' => '1e-51',
		'bit_score' => '196',
		'alignment_length' => '712',
		'identity_percentage' => '24.58',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'gsu19480' => array(
		'gene_id' => 'gsu19480',
		'e_value' => '2e-49',
		'bit_score' => '187',
		'alignment_length' => '422',
		'identity_percentage' => '32.46',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P007106'
		)
	),
	'gsu19500' => array(
		'gene_id' => 'gsu19500',
		'e_value' => '1e-48',
		'bit_score' => '184',
		'alignment_length' => '425',
		'identity_percentage' => '32.24',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P007106'
		)
	),
	'pte340320' => array(
		'gene_id' => 'pte340320',
		'e_value' => '2e-44',
		'bit_score' => '175',
		'alignment_length' => '712',
		'identity_percentage' => '23.74',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'CNC64A_282G00010' => array(
		'gene_id' => 'CNC64A_282G00010',
		'e_value' => '6e-43',
		'bit_score' => '166',
		'alignment_length' => '360',
		'identity_percentage' => '30.28',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P001532'
		)
	),
	'ccr103000' => array(
		'gene_id' => 'ccr103000',
		'e_value' => '9e-38',
		'bit_score' => '153',
		'alignment_length' => '396',
		'identity_percentage' => '31.31',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P007106'
		)
	),
	'ccr153840' => array(
		'gene_id' => 'ccr153840',
		'e_value' => '2e-37',
		'bit_score' => '152',
		'alignment_length' => '387',
		'identity_percentage' => '28.68',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P007106'
		)
	),
	'gsu44220' => array(
		'gene_id' => 'gsu44220',
		'e_value' => '4e-37',
		'bit_score' => '151',
		'alignment_length' => '411',
		'identity_percentage' => '27.49',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P028710'
		)
	),
	'gsu86670' => array(
		'gene_id' => 'gsu86670',
		'e_value' => '1e-35',
		'bit_score' => '147',
		'alignment_length' => '458',
		'identity_percentage' => '27.51',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027778'
		)
	),
	'CM17G00540' => array(
		'gene_id' => 'CM17G00540',
		'e_value' => '9e-35',
		'bit_score' => '145',
		'alignment_length' => '500',
		'identity_percentage' => '24.60',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P028710'
		)
	),
	'ES0090G00200' => array(
		'gene_id' => 'ES0090G00200',
		'e_value' => '8e-26',
		'bit_score' => '117',
		'alignment_length' => '383',
		'identity_percentage' => '26.89',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P028710'
		)
	),
	'Naga_100051g14' => array(
		'gene_id' => 'Naga_100051g14',
		'e_value' => '2e-25',
		'bit_score' => '116',
		'alignment_length' => '393',
		'identity_percentage' => '27.99',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P028710'
		)
	),
	'CM20G02610' => array(
		'gene_id' => 'CM20G02610',
		'e_value' => '1e-23',
		'bit_score' => '109',
		'alignment_length' => '205',
		'identity_percentage' => '34.15',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027778'
		)
	),
	'ES0100G00250' => array(
		'gene_id' => 'ES0100G00250',
		'e_value' => '1e-20',
		'bit_score' => '100',
		'alignment_length' => '454',
		'identity_percentage' => '24.01',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027778'
		)
	),
	'gsu73670' => array(
		'gene_id' => 'gsu73670',
		'e_value' => '8e-17',
		'bit_score' => '88.6',
		'alignment_length' => '376',
		'identity_percentage' => '24.73',
		'species' => 'gsu',
		'common_name' => 'Galdieria sulphuraria',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P063471'
		)
	),
	'CM04G01010' => array(
		'gene_id' => 'CM04G01010',
		'e_value' => '3e-16',
		'bit_score' => '87.0',
		'alignment_length' => '471',
		'identity_percentage' => '22.72',
		'species' => 'cme',
		'common_name' => 'Cyanidioschyzon merolae',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P027252'
		)
	),
	'pte547680' => array(
		'gene_id' => 'pte547680',
		'e_value' => '7e-10',
		'bit_score' => '67.0',
		'alignment_length' => '99',
		'identity_percentage' => '36.36',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P022080'
		)
	),
	'pte537960' => array(
		'gene_id' => 'pte537960',
		'e_value' => '2e-09',
		'bit_score' => '65.5',
		'alignment_length' => '133',
		'identity_percentage' => '33.08',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte142860' => array(
		'gene_id' => 'pte142860',
		'e_value' => '5e-09',
		'bit_score' => '64.3',
		'alignment_length' => '99',
		'identity_percentage' => '41.41',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte702950' => array(
		'gene_id' => 'pte702950',
		'e_value' => '7e-09',
		'bit_score' => '63.9',
		'alignment_length' => '99',
		'identity_percentage' => '36.36',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'ccr123160' => array(
		'gene_id' => 'ccr123160',
		'e_value' => '1e-08',
		'bit_score' => '62.4',
		'alignment_length' => '429',
		'identity_percentage' => '20.75',
		'species' => 'ccr',
		'common_name' => 'Chondrus crispus',
		'gf' => array(
			'HOMFAM' => 'HOM03P001314',
			'ORTHOFAM' => 'ORTHO03P063471'
		)
	),
	'pte716670' => array(
		'gene_id' => 'pte716670',
		'e_value' => '2e-08',
		'bit_score' => '62.8',
		'alignment_length' => '97',
		'identity_percentage' => '36.08',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte301520' => array(
		'gene_id' => 'pte301520',
		'e_value' => '2e-07',
		'bit_score' => '59.3',
		'alignment_length' => '216',
		'identity_percentage' => '30.09',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P010876',
			'ORTHOFAM' => 'ORTHO03P011814'
		)
	),
	'pte548020' => array(
		'gene_id' => 'pte548020',
		'e_value' => '3e-07',
		'bit_score' => '58.2',
		'alignment_length' => '99',
		'identity_percentage' => '33.33',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte215230' => array(
		'gene_id' => 'pte215230',
		'e_value' => '3e-06',
		'bit_score' => '55.5',
		'alignment_length' => '99',
		'identity_percentage' => '33.33',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	),
	'pte446270' => array(
		'gene_id' => 'pte446270',
		'e_value' => '4e-06',
		'bit_score' => '55.1',
		'alignment_length' => '99',
		'identity_percentage' => '37.37',
		'species' => 'pte',
		'common_name' => 'Paramecium tetraurelia',
		'gf' => array(
			'HOMFAM' => 'HOM03P004093',
			'ORTHOFAM' => 'ORTHO03P004653'
		)
	)
)
$similarity_hits_species = array(
	'ath' => array(
		(int) 0 => 'AT3G13870',
		(int) 1 => 'AT1G72960',
		(int) 2 => 'AT5G45160'
	),
	'osa' => array(
		(int) 0 => 'OS01G39310',
		(int) 1 => 'OS12G41170',
		(int) 2 => 'OS11G37260'
	),
	'atr' => array(
		(int) 0 => 'ATR_00064G00790',
		(int) 1 => 'ATR_00019G03700',
		(int) 2 => 'ATR_00002G06160'
	),
	'ppa' => array(
		(int) 0 => 'PP00382G00080',
		(int) 1 => 'PP00132G00620',
		(int) 2 => 'PP00033G01040',
		(int) 3 => 'PP00227G00230'
	),
	'cvu' => array(
		(int) 0 => 'CV00G45150'
	),
	'prcc4223' => array(
		(int) 0 => 'RCC4223.11g01590'
	),
	'pse3' => array(
		(int) 0 => 'PI00G12780'
	),
	'vca' => array(
		(int) 0 => 'VC00G21920'
	),
	'acg' => array(
		(int) 0 => 'AC00G64910'
	),
	'cre' => array(
		(int) 0 => 'CR10G04770'
	),
	'ome' => array(
		(int) 0 => 'OM_02G00590'
	),
	'olu' => array(
		(int) 0 => 'OL04G00500'
	),
	'ota' => array(
		(int) 0 => 'OT_04G00540'
	),
	'mrcc299' => array(
		(int) 0 => 'MRCC299_09G06070'
	),
	'orcc809' => array(
		(int) 0 => 'ORCC809_04G04660'
	),
	'bprrcc1105' => array(
		(int) 0 => 'BPRRCC1105_18G00790'
	),
	'mpu' => array(
		(int) 0 => 'MP18G00260'
	),
	'apr' => array(
		(int) 0 => 'AP00G56970'
	),
	'hsp' => array(
		(int) 0 => 'HE0000G07250'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0279823'
	),
	'sac' => array(
		(int) 0 => 'YOR165W'
	),
	'gsu' => array(
		(int) 0 => 'gsu43150',
		(int) 1 => 'gsu19480',
		(int) 2 => 'gsu19500',
		(int) 3 => 'gsu44220',
		(int) 4 => 'gsu86670',
		(int) 5 => 'gsu73670'
	),
	'ccr' => array(
		(int) 0 => 'ccr166320',
		(int) 1 => 'ccr134780',
		(int) 2 => 'ccr103000',
		(int) 3 => 'ccr153840',
		(int) 4 => 'ccr123160'
	),
	'scp' => array(
		(int) 0 => 'SPAC222.14c'
	),
	'cme' => array(
		(int) 0 => 'CM14G01410',
		(int) 1 => 'CM17G00540',
		(int) 2 => 'CM20G02610',
		(int) 3 => 'CM04G01010'
	),
	'pte' => array(
		(int) 0 => 'pte204310',
		(int) 1 => 'pte340320',
		(int) 2 => 'pte547680',
		(int) 3 => 'pte537960',
		(int) 4 => 'pte142860',
		(int) 5 => 'pte702950',
		(int) 6 => 'pte716670',
		(int) 7 => 'pte301520',
		(int) 8 => 'pte548020',
		(int) 9 => 'pte215230',
		(int) 10 => 'pte446270'
	),
	'esi' => array(
		(int) 0 => 'ES0090G00200',
		(int) 1 => 'ES0100G00250'
	),
	'nga' => array(
		(int) 0 => 'Naga_100051g14'
	)
)
$gene_id = 'AT3G13870'
$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 = 'AT3G13870'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'OM_07G00390'
$gf_placeholder = 'HOM03P000971'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_282G00010',
	'e_value' => '6e-43',
	'bit_score' => '166',
	'alignment_length' => '360',
	'identity_percentage' => '30.28',
	'gf' => array(
		'HOMFAM' => 'HOM03P001314',
		'ORTHOFAM' => 'ORTHO03P001532'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_282G00010'
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