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(
		'AT1G13340' => array(
			'gene_id' => 'AT1G13340',
			'e_value' => '0.0',
			'bit_score' => '840',
			'alignment_length' => '410',
			'identity_percentage' => '100.00',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00002G00640' => array(
			'gene_id' => 'ATR_00002G00640',
			'e_value' => '1e-55',
			'bit_score' => '198',
			'alignment_length' => '186',
			'identity_percentage' => '49.46',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G50210' => array(
			'gene_id' => 'OS03G50210',
			'e_value' => '5e-47',
			'bit_score' => '170',
			'alignment_length' => '183',
			'identity_percentage' => '46.99',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00079G00210' => array(
			'gene_id' => 'PP00079G00210',
			'e_value' => '9e-40',
			'bit_score' => '154',
			'alignment_length' => '192',
			'identity_percentage' => '39.58',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00030G00310' => array(
			'gene_id' => 'PP00030G00310',
			'e_value' => '4e-39',
			'bit_score' => '152',
			'alignment_length' => '190',
			'identity_percentage' => '37.89',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00036G01680' => array(
			'gene_id' => 'ATR_00036G01680',
			'e_value' => '2e-31',
			'bit_score' => '132',
			'alignment_length' => '175',
			'identity_percentage' => '36.00',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS01G49350' => array(
			'gene_id' => 'OS01G49350',
			'e_value' => '7e-31',
			'bit_score' => '125',
			'alignment_length' => '194',
			'identity_percentage' => '32.47',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS08G07830' => array(
			'gene_id' => 'OS08G07830',
			'e_value' => '8e-31',
			'bit_score' => '127',
			'alignment_length' => '176',
			'identity_percentage' => '35.80',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT4G35730' => array(
			'gene_id' => 'AT4G35730',
			'e_value' => '1e-29',
			'bit_score' => '123',
			'alignment_length' => '188',
			'identity_percentage' => '33.51',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00001G02660' => array(
			'gene_id' => 'ATR_00001G02660',
			'e_value' => '2e-29',
			'bit_score' => '125',
			'alignment_length' => '167',
			'identity_percentage' => '36.53',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00095G00370' => array(
			'gene_id' => 'PP00095G00370',
			'e_value' => '3e-29',
			'bit_score' => '125',
			'alignment_length' => '180',
			'identity_percentage' => '33.89',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT2G19710' => array(
			'gene_id' => 'AT2G19710',
			'e_value' => '9e-29',
			'bit_score' => '123',
			'alignment_length' => '181',
			'identity_percentage' => '34.81',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G25420' => array(
			'gene_id' => 'AT1G25420',
			'e_value' => '3e-28',
			'bit_score' => '117',
			'alignment_length' => '190',
			'identity_percentage' => '33.16',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS09G37510' => array(
			'gene_id' => 'OS09G37510',
			'e_value' => '9e-28',
			'bit_score' => '117',
			'alignment_length' => '171',
			'identity_percentage' => '33.92',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00079G00350' => array(
			'gene_id' => 'ATR_00079G00350',
			'e_value' => '4e-27',
			'bit_score' => '114',
			'alignment_length' => '149',
			'identity_percentage' => '36.91',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS01G51010' => array(
			'gene_id' => 'OS01G51010',
			'e_value' => '4e-27',
			'bit_score' => '118',
			'alignment_length' => '179',
			'identity_percentage' => '31.84',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G15230' => array(
			'gene_id' => 'OS03G15230',
			'e_value' => '2e-26',
			'bit_score' => '115',
			'alignment_length' => '230',
			'identity_percentage' => '32.61',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G34220' => array(
			'gene_id' => 'AT1G34220',
			'e_value' => '2e-25',
			'bit_score' => '112',
			'alignment_length' => '220',
			'identity_percentage' => '29.09',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT4G29440' => array(
			'gene_id' => 'AT4G29440',
			'e_value' => '6e-25',
			'bit_score' => '111',
			'alignment_length' => '180',
			'identity_percentage' => '31.67',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G15210' => array(
			'gene_id' => 'OS03G15210',
			'e_value' => '2e-24',
			'bit_score' => '103',
			'alignment_length' => '174',
			'identity_percentage' => '35.06',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G15220' => array(
			'gene_id' => 'OS03G15220',
			'e_value' => '9e-23',
			'bit_score' => '99.0',
			'alignment_length' => '174',
			'identity_percentage' => '33.91',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00003G02620' => array(
			'gene_id' => 'ATR_00003G02620',
			'e_value' => '1e-21',
			'bit_score' => '101',
			'alignment_length' => '171',
			'identity_percentage' => '32.16',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR10G03920' => array(
			'gene_id' => 'CR10G03920',
			'e_value' => '1e-21',
			'bit_score' => '100',
			'alignment_length' => '219',
			'identity_percentage' => '27.85',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT2G14830' => array(
			'gene_id' => 'AT2G14830',
			'e_value' => '6e-21',
			'bit_score' => '97.8',
			'alignment_length' => '173',
			'identity_percentage' => '31.21',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G79910' => array(
			'gene_id' => 'AT1G79910',
			'e_value' => '7e-21',
			'bit_score' => '97.1',
			'alignment_length' => '178',
			'identity_percentage' => '28.65',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'phs256930' => array(
			'gene_id' => 'phs256930',
			'e_value' => '8e-21',
			'bit_score' => '95.9',
			'alignment_length' => '181',
			'identity_percentage' => '34.25',
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00200G00070' => array(
			'gene_id' => 'ATR_00200G00070',
			'e_value' => '1e-20',
			'bit_score' => '98.2',
			'alignment_length' => '175',
			'identity_percentage' => '33.14',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00010G02880' => array(
			'gene_id' => 'ATR_00010G02880',
			'e_value' => '3e-20',
			'bit_score' => '96.7',
			'alignment_length' => '148',
			'identity_percentage' => '34.46',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100136g20' => array(
			'gene_id' => 'Naga_100136g20',
			'e_value' => '9e-20',
			'bit_score' => '92.4',
			'alignment_length' => '212',
			'identity_percentage' => '27.83',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00043G00230' => array(
			'gene_id' => 'PP00043G00230',
			'e_value' => '2e-18',
			'bit_score' => '91.7',
			'alignment_length' => '174',
			'identity_percentage' => '25.86',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G64720' => array(
			'gene_id' => 'VC00G64720',
			'e_value' => '3e-18',
			'bit_score' => '90.5',
			'alignment_length' => '185',
			'identity_percentage' => '29.19',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MP17G00050' => array(
			'gene_id' => 'MP17G00050',
			'e_value' => '8e-18',
			'bit_score' => '88.6',
			'alignment_length' => '210',
			'identity_percentage' => '28.10',
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP19G02370' => array(
			'gene_id' => 'TP19G02370',
			'e_value' => '3e-17',
			'bit_score' => '83.2',
			'alignment_length' => '174',
			'identity_percentage' => '29.89',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0289029' => array(
			'gene_id' => 'DDB_G0289029',
			'e_value' => '7e-17',
			'bit_score' => '85.5',
			'alignment_length' => '178',
			'identity_percentage' => '31.46',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0031G00390' => array(
			'gene_id' => 'ES0031G00390',
			'e_value' => '1e-16',
			'bit_score' => '85.5',
			'alignment_length' => '173',
			'identity_percentage' => '27.75',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G60260' => array(
			'gene_id' => 'CV00G60260',
			'e_value' => '1e-16',
			'bit_score' => '85.5',
			'alignment_length' => '173',
			'identity_percentage' => '30.64',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G52315' => array(
			'gene_id' => 'AT1G52315',
			'e_value' => '1e-16',
			'bit_score' => '84.3',
			'alignment_length' => '179',
			'identity_percentage' => '27.93',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0284389' => array(
			'gene_id' => 'DDB_G0284389',
			'e_value' => '7e-16',
			'bit_score' => '84.0',
			'alignment_length' => '172',
			'identity_percentage' => '30.23',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS02G06430' => array(
			'gene_id' => 'OS02G06430',
			'e_value' => '2e-15',
			'bit_score' => '82.4',
			'alignment_length' => '180',
			'identity_percentage' => '27.22',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT4G32350' => array(
			'gene_id' => 'AT4G32350',
			'e_value' => '3e-15',
			'bit_score' => '81.6',
			'alignment_length' => '178',
			'identity_percentage' => '27.53',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS06G47250' => array(
			'gene_id' => 'OS06G47250',
			'e_value' => '4e-15',
			'bit_score' => '81.6',
			'alignment_length' => '179',
			'identity_percentage' => '27.93',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OM_09G01680' => array(
			'gene_id' => 'OM_09G01680',
			'e_value' => '9e-15',
			'bit_score' => '79.0',
			'alignment_length' => '181',
			'identity_percentage' => '27.62',
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_05G04260' => array(
			'gene_id' => 'PTI_05G04260',
			'e_value' => '5e-14',
			'bit_score' => '76.6',
			'alignment_length' => '167',
			'identity_percentage' => '25.15',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'HE0000G04150' => array(
			'gene_id' => 'HE0000G04150',
			'e_value' => '2e-13',
			'bit_score' => '72.4',
			'alignment_length' => '125',
			'identity_percentage' => '28.00',
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0002G00430' => array(
			'gene_id' => 'AA0002G00430',
			'e_value' => '3e-13',
			'bit_score' => '72.0',
			'alignment_length' => '168',
			'identity_percentage' => '29.17',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G00640' => array(
			'gene_id' => 'AP00G00640',
			'e_value' => '5e-13',
			'bit_score' => '73.9',
			'alignment_length' => '199',
			'identity_percentage' => '29.15',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G94970' => array(
			'gene_id' => 'AC00G94970',
			'e_value' => '2e-12',
			'bit_score' => '71.6',
			'alignment_length' => '180',
			'identity_percentage' => '26.11',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT3G15490' => array(
			'gene_id' => 'AT3G15490',
			'e_value' => '3e-12',
			'bit_score' => '69.3',
			'alignment_length' => '130',
			'identity_percentage' => '33.08',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G94960' => array(
			'gene_id' => 'AC00G94960',
			'e_value' => '8e-12',
			'bit_score' => '68.6',
			'alignment_length' => '180',
			'identity_percentage' => '26.11',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00010736' => array(
			'gene_id' => 'WBGene00010736',
			'e_value' => '2e-11',
			'bit_score' => '69.3',
			'alignment_length' => '174',
			'identity_percentage' => '26.44',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000031729' => array(
			'gene_id' => 'ENSMUSG00000031729',
			'e_value' => '2e-11',
			'bit_score' => '68.9',
			'alignment_length' => '183',
			'identity_percentage' => '26.23',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL03G01580' => array(
			'gene_id' => 'OL03G01580',
			'e_value' => '3e-11',
			'bit_score' => '68.2',
			'alignment_length' => '180',
			'identity_percentage' => '26.67',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0035715' => array(
			'gene_id' => 'FBgn0035715',
			'e_value' => '1e-09',
			'bit_score' => '63.5',
			'alignment_length' => '173',
			'identity_percentage' => '24.86',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ORCC809_03G01460' => array(
			'gene_id' => 'ORCC809_03G01460',
			'e_value' => '3e-09',
			'bit_score' => '62.4',
			'alignment_length' => '175',
			'identity_percentage' => '29.14',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_044G00100' => array(
			'gene_id' => 'CNC64A_044G00100',
			'e_value' => '2e-08',
			'bit_score' => '60.1',
			'alignment_length' => '192',
			'identity_percentage' => '23.96',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'BPRRCC1105_12G02820' => array(
			'gene_id' => 'BPRRCC1105_12G02820',
			'e_value' => '6e-08',
			'bit_score' => '58.2',
			'alignment_length' => '163',
			'identity_percentage' => '23.93',
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YNL265C' => array(
			'gene_id' => 'YNL265C',
			'e_value' => '3e-06',
			'bit_score' => '52.8',
			'alignment_length' => '173',
			'identity_percentage' => '26.01',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G51900' => array(
			'gene_id' => 'AT1G51900',
			'e_value' => '7e-06',
			'bit_score' => '52.4',
			'alignment_length' => '188',
			'identity_percentage' => '25.00',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'ath' => array(
			(int) 0 => 'AT1G13340',
			(int) 1 => 'AT4G35730',
			(int) 2 => 'AT2G19710',
			(int) 3 => 'AT1G25420',
			(int) 4 => 'AT1G34220',
			(int) 5 => 'AT4G29440',
			(int) 6 => 'AT2G14830',
			(int) 7 => 'AT1G79910',
			(int) 8 => 'AT1G52315',
			(int) 9 => 'AT4G32350',
			(int) 10 => 'AT3G15490',
			(int) 11 => 'AT1G51900'
		),
		'atr' => array(
			(int) 0 => 'ATR_00002G00640',
			(int) 1 => 'ATR_00036G01680',
			(int) 2 => 'ATR_00001G02660',
			(int) 3 => 'ATR_00079G00350',
			(int) 4 => 'ATR_00003G02620',
			(int) 5 => 'ATR_00200G00070',
			(int) 6 => 'ATR_00010G02880'
		),
		'osa' => array(
			(int) 0 => 'OS03G50210',
			(int) 1 => 'OS01G49350',
			(int) 2 => 'OS08G07830',
			(int) 3 => 'OS09G37510',
			(int) 4 => 'OS01G51010',
			(int) 5 => 'OS03G15230',
			(int) 6 => 'OS03G15210',
			(int) 7 => 'OS03G15220',
			(int) 8 => 'OS02G06430',
			(int) 9 => 'OS06G47250'
		),
		'ppa' => array(
			(int) 0 => 'PP00079G00210',
			(int) 1 => 'PP00030G00310',
			(int) 2 => 'PP00095G00370',
			(int) 3 => 'PP00043G00230'
		),
		'cre' => array(
			(int) 0 => 'CR10G03920'
		),
		'phs' => array(
			(int) 0 => 'phs256930'
		),
		'nga' => array(
			(int) 0 => 'Naga_100136g20'
		),
		'vca' => array(
			(int) 0 => 'VC00G64720'
		),
		'mpu' => array(
			(int) 0 => 'MP17G00050'
		),
		'tps' => array(
			(int) 0 => 'TP19G02370'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0289029',
			(int) 1 => 'DDB_G0284389'
		),
		'esi' => array(
			(int) 0 => 'ES0031G00390'
		),
		'cvu' => array(
			(int) 0 => 'CV00G60260'
		),
		'ome' => array(
			(int) 0 => 'OM_09G01680'
		),
		'ptri' => array(
			(int) 0 => 'PTI_05G04260'
		),
		'hsp' => array(
			(int) 0 => 'HE0000G04150'
		),
		'aan' => array(
			(int) 0 => 'AA0002G00430'
		),
		'apr' => array(
			(int) 0 => 'AP00G00640'
		),
		'acg' => array(
			(int) 0 => 'AC00G94970',
			(int) 1 => 'AC00G94960'
		),
		'cel' => array(
			(int) 0 => 'WBGene00010736'
		),
		'mus' => array(
			(int) 0 => 'ENSMUSG00000031729'
		),
		'olu' => array(
			(int) 0 => 'OL03G01580'
		),
		'drm' => array(
			(int) 0 => 'FBgn0035715'
		),
		'orcc809' => array(
			(int) 0 => 'ORCC809_03G01460'
		),
		'bprrcc1105' => array(
			(int) 0 => 'BPRRCC1105_12G02820'
		),
		'sac' => array(
			(int) 0 => 'YNL265C'
		)
	),
	'gene_id' => 'AT1G13340',
	'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' => 'AT1G13340',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'AC00G28340',
	'gf_placeholder' => 'HOM03P007610',
	'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(
	'AT1G13340' => array(
		'gene_id' => 'AT1G13340',
		'e_value' => '0.0',
		'bit_score' => '840',
		'alignment_length' => '410',
		'identity_percentage' => '100.00',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P042457'
		)
	),
	'ATR_00002G00640' => array(
		'gene_id' => 'ATR_00002G00640',
		'e_value' => '1e-55',
		'bit_score' => '198',
		'alignment_length' => '186',
		'identity_percentage' => '49.46',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P042457'
		)
	),
	'OS03G50210' => array(
		'gene_id' => 'OS03G50210',
		'e_value' => '5e-47',
		'bit_score' => '170',
		'alignment_length' => '183',
		'identity_percentage' => '46.99',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P042457'
		)
	),
	'PP00079G00210' => array(
		'gene_id' => 'PP00079G00210',
		'e_value' => '9e-40',
		'bit_score' => '154',
		'alignment_length' => '192',
		'identity_percentage' => '39.58',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'PP00030G00310' => array(
		'gene_id' => 'PP00030G00310',
		'e_value' => '4e-39',
		'bit_score' => '152',
		'alignment_length' => '190',
		'identity_percentage' => '37.89',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ATR_00036G01680' => array(
		'gene_id' => 'ATR_00036G01680',
		'e_value' => '2e-31',
		'bit_score' => '132',
		'alignment_length' => '175',
		'identity_percentage' => '36.00',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'OS01G49350' => array(
		'gene_id' => 'OS01G49350',
		'e_value' => '7e-31',
		'bit_score' => '125',
		'alignment_length' => '194',
		'identity_percentage' => '32.47',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P039350'
		)
	),
	'OS08G07830' => array(
		'gene_id' => 'OS08G07830',
		'e_value' => '8e-31',
		'bit_score' => '127',
		'alignment_length' => '176',
		'identity_percentage' => '35.80',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT4G35730' => array(
		'gene_id' => 'AT4G35730',
		'e_value' => '1e-29',
		'bit_score' => '123',
		'alignment_length' => '188',
		'identity_percentage' => '33.51',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P066330'
		)
	),
	'ATR_00001G02660' => array(
		'gene_id' => 'ATR_00001G02660',
		'e_value' => '2e-29',
		'bit_score' => '125',
		'alignment_length' => '167',
		'identity_percentage' => '36.53',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P010073'
		)
	),
	'PP00095G00370' => array(
		'gene_id' => 'PP00095G00370',
		'e_value' => '3e-29',
		'bit_score' => '125',
		'alignment_length' => '180',
		'identity_percentage' => '33.89',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P087707'
		)
	),
	'AT2G19710' => array(
		'gene_id' => 'AT2G19710',
		'e_value' => '9e-29',
		'bit_score' => '123',
		'alignment_length' => '181',
		'identity_percentage' => '34.81',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P049438'
		)
	),
	'AT1G25420' => array(
		'gene_id' => 'AT1G25420',
		'e_value' => '3e-28',
		'bit_score' => '117',
		'alignment_length' => '190',
		'identity_percentage' => '33.16',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P039350'
		)
	),
	'OS09G37510' => array(
		'gene_id' => 'OS09G37510',
		'e_value' => '9e-28',
		'bit_score' => '117',
		'alignment_length' => '171',
		'identity_percentage' => '33.92',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P066330'
		)
	),
	'ATR_00079G00350' => array(
		'gene_id' => 'ATR_00079G00350',
		'e_value' => '4e-27',
		'bit_score' => '114',
		'alignment_length' => '149',
		'identity_percentage' => '36.91',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P039350'
		)
	),
	'OS01G51010' => array(
		'gene_id' => 'OS01G51010',
		'e_value' => '4e-27',
		'bit_score' => '118',
		'alignment_length' => '179',
		'identity_percentage' => '31.84',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'OS03G15230' => array(
		'gene_id' => 'OS03G15230',
		'e_value' => '2e-26',
		'bit_score' => '115',
		'alignment_length' => '230',
		'identity_percentage' => '32.61',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P034414'
		)
	),
	'AT1G34220' => array(
		'gene_id' => 'AT1G34220',
		'e_value' => '2e-25',
		'bit_score' => '112',
		'alignment_length' => '220',
		'identity_percentage' => '29.09',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT4G29440' => array(
		'gene_id' => 'AT4G29440',
		'e_value' => '6e-25',
		'bit_score' => '111',
		'alignment_length' => '180',
		'identity_percentage' => '31.67',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P049438'
		)
	),
	'OS03G15210' => array(
		'gene_id' => 'OS03G15210',
		'e_value' => '2e-24',
		'bit_score' => '103',
		'alignment_length' => '174',
		'identity_percentage' => '35.06',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P034414'
		)
	),
	'OS03G15220' => array(
		'gene_id' => 'OS03G15220',
		'e_value' => '9e-23',
		'bit_score' => '99.0',
		'alignment_length' => '174',
		'identity_percentage' => '33.91',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P034414'
		)
	),
	'ATR_00003G02620' => array(
		'gene_id' => 'ATR_00003G02620',
		'e_value' => '1e-21',
		'bit_score' => '101',
		'alignment_length' => '171',
		'identity_percentage' => '32.16',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P183665'
		)
	),
	'CR10G03920' => array(
		'gene_id' => 'CR10G03920',
		'e_value' => '1e-21',
		'bit_score' => '100',
		'alignment_length' => '219',
		'identity_percentage' => '27.85',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT2G14830' => array(
		'gene_id' => 'AT2G14830',
		'e_value' => '6e-21',
		'bit_score' => '97.8',
		'alignment_length' => '173',
		'identity_percentage' => '31.21',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P051073'
		)
	),
	'AT1G79910' => array(
		'gene_id' => 'AT1G79910',
		'e_value' => '7e-21',
		'bit_score' => '97.1',
		'alignment_length' => '178',
		'identity_percentage' => '28.65',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P075682'
		)
	),
	'phs256930' => array(
		'gene_id' => 'phs256930',
		'e_value' => '8e-21',
		'bit_score' => '95.9',
		'alignment_length' => '181',
		'identity_percentage' => '34.25',
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ATR_00200G00070' => array(
		'gene_id' => 'ATR_00200G00070',
		'e_value' => '1e-20',
		'bit_score' => '98.2',
		'alignment_length' => '175',
		'identity_percentage' => '33.14',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P075682'
		)
	),
	'ATR_00010G02880' => array(
		'gene_id' => 'ATR_00010G02880',
		'e_value' => '3e-20',
		'bit_score' => '96.7',
		'alignment_length' => '148',
		'identity_percentage' => '34.46',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P206020'
		)
	),
	'Naga_100136g20' => array(
		'gene_id' => 'Naga_100136g20',
		'e_value' => '9e-20',
		'bit_score' => '92.4',
		'alignment_length' => '212',
		'identity_percentage' => '27.83',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'PP00043G00230' => array(
		'gene_id' => 'PP00043G00230',
		'e_value' => '2e-18',
		'bit_score' => '91.7',
		'alignment_length' => '174',
		'identity_percentage' => '25.86',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P158453'
		)
	),
	'VC00G64720' => array(
		'gene_id' => 'VC00G64720',
		'e_value' => '3e-18',
		'bit_score' => '90.5',
		'alignment_length' => '185',
		'identity_percentage' => '29.19',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'MP17G00050' => array(
		'gene_id' => 'MP17G00050',
		'e_value' => '8e-18',
		'bit_score' => '88.6',
		'alignment_length' => '210',
		'identity_percentage' => '28.10',
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'TP19G02370' => array(
		'gene_id' => 'TP19G02370',
		'e_value' => '3e-17',
		'bit_score' => '83.2',
		'alignment_length' => '174',
		'identity_percentage' => '29.89',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'DDB_G0289029' => array(
		'gene_id' => 'DDB_G0289029',
		'e_value' => '7e-17',
		'bit_score' => '85.5',
		'alignment_length' => '178',
		'identity_percentage' => '31.46',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ES0031G00390' => array(
		'gene_id' => 'ES0031G00390',
		'e_value' => '1e-16',
		'bit_score' => '85.5',
		'alignment_length' => '173',
		'identity_percentage' => '27.75',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'CV00G60260' => array(
		'gene_id' => 'CV00G60260',
		'e_value' => '1e-16',
		'bit_score' => '85.5',
		'alignment_length' => '173',
		'identity_percentage' => '30.64',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT1G52315' => array(
		'gene_id' => 'AT1G52315',
		'e_value' => '1e-16',
		'bit_score' => '84.3',
		'alignment_length' => '179',
		'identity_percentage' => '27.93',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P116121'
		)
	),
	'DDB_G0284389' => array(
		'gene_id' => 'DDB_G0284389',
		'e_value' => '7e-16',
		'bit_score' => '84.0',
		'alignment_length' => '172',
		'identity_percentage' => '30.23',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P000055',
			'ORTHOFAM' => 'ORTHO03P103792'
		)
	),
	'OS02G06430' => array(
		'gene_id' => 'OS02G06430',
		'e_value' => '2e-15',
		'bit_score' => '82.4',
		'alignment_length' => '180',
		'identity_percentage' => '27.22',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P049023'
		)
	),
	'AT4G32350' => array(
		'gene_id' => 'AT4G32350',
		'e_value' => '3e-15',
		'bit_score' => '81.6',
		'alignment_length' => '178',
		'identity_percentage' => '27.53',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P095477'
		)
	),
	'OS06G47250' => array(
		'gene_id' => 'OS06G47250',
		'e_value' => '4e-15',
		'bit_score' => '81.6',
		'alignment_length' => '179',
		'identity_percentage' => '27.93',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P049023'
		)
	),
	'OM_09G01680' => array(
		'gene_id' => 'OM_09G01680',
		'e_value' => '9e-15',
		'bit_score' => '79.0',
		'alignment_length' => '181',
		'identity_percentage' => '27.62',
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'PTI_05G04260' => array(
		'gene_id' => 'PTI_05G04260',
		'e_value' => '5e-14',
		'bit_score' => '76.6',
		'alignment_length' => '167',
		'identity_percentage' => '25.15',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'HE0000G04150' => array(
		'gene_id' => 'HE0000G04150',
		'e_value' => '2e-13',
		'bit_score' => '72.4',
		'alignment_length' => '125',
		'identity_percentage' => '28.00',
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AA0002G00430' => array(
		'gene_id' => 'AA0002G00430',
		'e_value' => '3e-13',
		'bit_score' => '72.0',
		'alignment_length' => '168',
		'identity_percentage' => '29.17',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AP00G00640' => array(
		'gene_id' => 'AP00G00640',
		'e_value' => '5e-13',
		'bit_score' => '73.9',
		'alignment_length' => '199',
		'identity_percentage' => '29.15',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AC00G94970' => array(
		'gene_id' => 'AC00G94970',
		'e_value' => '2e-12',
		'bit_score' => '71.6',
		'alignment_length' => '180',
		'identity_percentage' => '26.11',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT3G15490' => array(
		'gene_id' => 'AT3G15490',
		'e_value' => '3e-12',
		'bit_score' => '69.3',
		'alignment_length' => '130',
		'identity_percentage' => '33.08',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P175619'
		)
	),
	'AC00G94960' => array(
		'gene_id' => 'AC00G94960',
		'e_value' => '8e-12',
		'bit_score' => '68.6',
		'alignment_length' => '180',
		'identity_percentage' => '26.11',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'WBGene00010736' => array(
		'gene_id' => 'WBGene00010736',
		'e_value' => '2e-11',
		'bit_score' => '69.3',
		'alignment_length' => '174',
		'identity_percentage' => '26.44',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ENSMUSG00000031729' => array(
		'gene_id' => 'ENSMUSG00000031729',
		'e_value' => '2e-11',
		'bit_score' => '68.9',
		'alignment_length' => '183',
		'identity_percentage' => '26.23',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'OL03G01580' => array(
		'gene_id' => 'OL03G01580',
		'e_value' => '3e-11',
		'bit_score' => '68.2',
		'alignment_length' => '180',
		'identity_percentage' => '26.67',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'FBgn0035715' => array(
		'gene_id' => 'FBgn0035715',
		'e_value' => '1e-09',
		'bit_score' => '63.5',
		'alignment_length' => '173',
		'identity_percentage' => '24.86',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ORCC809_03G01460' => array(
		'gene_id' => 'ORCC809_03G01460',
		'e_value' => '3e-09',
		'bit_score' => '62.4',
		'alignment_length' => '175',
		'identity_percentage' => '29.14',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'CNC64A_044G00100' => array(
		'gene_id' => 'CNC64A_044G00100',
		'e_value' => '2e-08',
		'bit_score' => '60.1',
		'alignment_length' => '192',
		'identity_percentage' => '23.96',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'BPRRCC1105_12G02820' => array(
		'gene_id' => 'BPRRCC1105_12G02820',
		'e_value' => '6e-08',
		'bit_score' => '58.2',
		'alignment_length' => '163',
		'identity_percentage' => '23.93',
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'YNL265C' => array(
		'gene_id' => 'YNL265C',
		'e_value' => '3e-06',
		'bit_score' => '52.8',
		'alignment_length' => '173',
		'identity_percentage' => '26.01',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT1G51900' => array(
		'gene_id' => 'AT1G51900',
		'e_value' => '7e-06',
		'bit_score' => '52.4',
		'alignment_length' => '188',
		'identity_percentage' => '25.00',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P051073'
		)
	)
)
$similarity_hits_species = array(
	'ath' => array(
		(int) 0 => 'AT1G13340',
		(int) 1 => 'AT4G35730',
		(int) 2 => 'AT2G19710',
		(int) 3 => 'AT1G25420',
		(int) 4 => 'AT1G34220',
		(int) 5 => 'AT4G29440',
		(int) 6 => 'AT2G14830',
		(int) 7 => 'AT1G79910',
		(int) 8 => 'AT1G52315',
		(int) 9 => 'AT4G32350',
		(int) 10 => 'AT3G15490',
		(int) 11 => 'AT1G51900'
	),
	'atr' => array(
		(int) 0 => 'ATR_00002G00640',
		(int) 1 => 'ATR_00036G01680',
		(int) 2 => 'ATR_00001G02660',
		(int) 3 => 'ATR_00079G00350',
		(int) 4 => 'ATR_00003G02620',
		(int) 5 => 'ATR_00200G00070',
		(int) 6 => 'ATR_00010G02880'
	),
	'osa' => array(
		(int) 0 => 'OS03G50210',
		(int) 1 => 'OS01G49350',
		(int) 2 => 'OS08G07830',
		(int) 3 => 'OS09G37510',
		(int) 4 => 'OS01G51010',
		(int) 5 => 'OS03G15230',
		(int) 6 => 'OS03G15210',
		(int) 7 => 'OS03G15220',
		(int) 8 => 'OS02G06430',
		(int) 9 => 'OS06G47250'
	),
	'ppa' => array(
		(int) 0 => 'PP00079G00210',
		(int) 1 => 'PP00030G00310',
		(int) 2 => 'PP00095G00370',
		(int) 3 => 'PP00043G00230'
	),
	'cre' => array(
		(int) 0 => 'CR10G03920'
	),
	'phs' => array(
		(int) 0 => 'phs256930'
	),
	'nga' => array(
		(int) 0 => 'Naga_100136g20'
	),
	'vca' => array(
		(int) 0 => 'VC00G64720'
	),
	'mpu' => array(
		(int) 0 => 'MP17G00050'
	),
	'tps' => array(
		(int) 0 => 'TP19G02370'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0289029',
		(int) 1 => 'DDB_G0284389'
	),
	'esi' => array(
		(int) 0 => 'ES0031G00390'
	),
	'cvu' => array(
		(int) 0 => 'CV00G60260'
	),
	'ome' => array(
		(int) 0 => 'OM_09G01680'
	),
	'ptri' => array(
		(int) 0 => 'PTI_05G04260'
	),
	'hsp' => array(
		(int) 0 => 'HE0000G04150'
	),
	'aan' => array(
		(int) 0 => 'AA0002G00430'
	),
	'apr' => array(
		(int) 0 => 'AP00G00640'
	),
	'acg' => array(
		(int) 0 => 'AC00G94970',
		(int) 1 => 'AC00G94960'
	),
	'cel' => array(
		(int) 0 => 'WBGene00010736'
	),
	'mus' => array(
		(int) 0 => 'ENSMUSG00000031729'
	),
	'olu' => array(
		(int) 0 => 'OL03G01580'
	),
	'drm' => array(
		(int) 0 => 'FBgn0035715'
	),
	'orcc809' => array(
		(int) 0 => 'ORCC809_03G01460'
	),
	'bprrcc1105' => array(
		(int) 0 => 'BPRRCC1105_12G02820'
	),
	'sac' => array(
		(int) 0 => 'YNL265C'
	)
)
$gene_id = 'AT1G13340'
$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 = 'AT1G13340'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'AC00G28340'
$gf_placeholder = 'HOM03P007610'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_044G00100',
	'e_value' => '2e-08',
	'bit_score' => '60.1',
	'alignment_length' => '192',
	'identity_percentage' => '23.96',
	'gf' => array(
		'HOMFAM' => 'HOM03P000893',
		'ORTHOFAM' => 'ORTHO03P001894'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00100'
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(
		'AT1G13340' => array(
			'gene_id' => 'AT1G13340',
			'e_value' => '0.0',
			'bit_score' => '840',
			'alignment_length' => '410',
			'identity_percentage' => '100.00',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00002G00640' => array(
			'gene_id' => 'ATR_00002G00640',
			'e_value' => '1e-55',
			'bit_score' => '198',
			'alignment_length' => '186',
			'identity_percentage' => '49.46',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G50210' => array(
			'gene_id' => 'OS03G50210',
			'e_value' => '5e-47',
			'bit_score' => '170',
			'alignment_length' => '183',
			'identity_percentage' => '46.99',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00079G00210' => array(
			'gene_id' => 'PP00079G00210',
			'e_value' => '9e-40',
			'bit_score' => '154',
			'alignment_length' => '192',
			'identity_percentage' => '39.58',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00030G00310' => array(
			'gene_id' => 'PP00030G00310',
			'e_value' => '4e-39',
			'bit_score' => '152',
			'alignment_length' => '190',
			'identity_percentage' => '37.89',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00036G01680' => array(
			'gene_id' => 'ATR_00036G01680',
			'e_value' => '2e-31',
			'bit_score' => '132',
			'alignment_length' => '175',
			'identity_percentage' => '36.00',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS01G49350' => array(
			'gene_id' => 'OS01G49350',
			'e_value' => '7e-31',
			'bit_score' => '125',
			'alignment_length' => '194',
			'identity_percentage' => '32.47',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS08G07830' => array(
			'gene_id' => 'OS08G07830',
			'e_value' => '8e-31',
			'bit_score' => '127',
			'alignment_length' => '176',
			'identity_percentage' => '35.80',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT4G35730' => array(
			'gene_id' => 'AT4G35730',
			'e_value' => '1e-29',
			'bit_score' => '123',
			'alignment_length' => '188',
			'identity_percentage' => '33.51',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00001G02660' => array(
			'gene_id' => 'ATR_00001G02660',
			'e_value' => '2e-29',
			'bit_score' => '125',
			'alignment_length' => '167',
			'identity_percentage' => '36.53',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00095G00370' => array(
			'gene_id' => 'PP00095G00370',
			'e_value' => '3e-29',
			'bit_score' => '125',
			'alignment_length' => '180',
			'identity_percentage' => '33.89',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT2G19710' => array(
			'gene_id' => 'AT2G19710',
			'e_value' => '9e-29',
			'bit_score' => '123',
			'alignment_length' => '181',
			'identity_percentage' => '34.81',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G25420' => array(
			'gene_id' => 'AT1G25420',
			'e_value' => '3e-28',
			'bit_score' => '117',
			'alignment_length' => '190',
			'identity_percentage' => '33.16',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS09G37510' => array(
			'gene_id' => 'OS09G37510',
			'e_value' => '9e-28',
			'bit_score' => '117',
			'alignment_length' => '171',
			'identity_percentage' => '33.92',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00079G00350' => array(
			'gene_id' => 'ATR_00079G00350',
			'e_value' => '4e-27',
			'bit_score' => '114',
			'alignment_length' => '149',
			'identity_percentage' => '36.91',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS01G51010' => array(
			'gene_id' => 'OS01G51010',
			'e_value' => '4e-27',
			'bit_score' => '118',
			'alignment_length' => '179',
			'identity_percentage' => '31.84',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G15230' => array(
			'gene_id' => 'OS03G15230',
			'e_value' => '2e-26',
			'bit_score' => '115',
			'alignment_length' => '230',
			'identity_percentage' => '32.61',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G34220' => array(
			'gene_id' => 'AT1G34220',
			'e_value' => '2e-25',
			'bit_score' => '112',
			'alignment_length' => '220',
			'identity_percentage' => '29.09',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT4G29440' => array(
			'gene_id' => 'AT4G29440',
			'e_value' => '6e-25',
			'bit_score' => '111',
			'alignment_length' => '180',
			'identity_percentage' => '31.67',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G15210' => array(
			'gene_id' => 'OS03G15210',
			'e_value' => '2e-24',
			'bit_score' => '103',
			'alignment_length' => '174',
			'identity_percentage' => '35.06',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS03G15220' => array(
			'gene_id' => 'OS03G15220',
			'e_value' => '9e-23',
			'bit_score' => '99.0',
			'alignment_length' => '174',
			'identity_percentage' => '33.91',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00003G02620' => array(
			'gene_id' => 'ATR_00003G02620',
			'e_value' => '1e-21',
			'bit_score' => '101',
			'alignment_length' => '171',
			'identity_percentage' => '32.16',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CR10G03920' => array(
			'gene_id' => 'CR10G03920',
			'e_value' => '1e-21',
			'bit_score' => '100',
			'alignment_length' => '219',
			'identity_percentage' => '27.85',
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT2G14830' => array(
			'gene_id' => 'AT2G14830',
			'e_value' => '6e-21',
			'bit_score' => '97.8',
			'alignment_length' => '173',
			'identity_percentage' => '31.21',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G79910' => array(
			'gene_id' => 'AT1G79910',
			'e_value' => '7e-21',
			'bit_score' => '97.1',
			'alignment_length' => '178',
			'identity_percentage' => '28.65',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'phs256930' => array(
			'gene_id' => 'phs256930',
			'e_value' => '8e-21',
			'bit_score' => '95.9',
			'alignment_length' => '181',
			'identity_percentage' => '34.25',
			'species' => 'phs',
			'common_name' => 'Phytophtora sojae',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00200G00070' => array(
			'gene_id' => 'ATR_00200G00070',
			'e_value' => '1e-20',
			'bit_score' => '98.2',
			'alignment_length' => '175',
			'identity_percentage' => '33.14',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ATR_00010G02880' => array(
			'gene_id' => 'ATR_00010G02880',
			'e_value' => '3e-20',
			'bit_score' => '96.7',
			'alignment_length' => '148',
			'identity_percentage' => '34.46',
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'Naga_100136g20' => array(
			'gene_id' => 'Naga_100136g20',
			'e_value' => '9e-20',
			'bit_score' => '92.4',
			'alignment_length' => '212',
			'identity_percentage' => '27.83',
			'species' => 'nga',
			'common_name' => 'Nannochloropsis gaditana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PP00043G00230' => array(
			'gene_id' => 'PP00043G00230',
			'e_value' => '2e-18',
			'bit_score' => '91.7',
			'alignment_length' => '174',
			'identity_percentage' => '25.86',
			'species' => 'ppa',
			'common_name' => 'Physcomitrella patens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'VC00G64720' => array(
			'gene_id' => 'VC00G64720',
			'e_value' => '3e-18',
			'bit_score' => '90.5',
			'alignment_length' => '185',
			'identity_percentage' => '29.19',
			'species' => 'vca',
			'common_name' => 'Volvox carteri',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'MP17G00050' => array(
			'gene_id' => 'MP17G00050',
			'e_value' => '8e-18',
			'bit_score' => '88.6',
			'alignment_length' => '210',
			'identity_percentage' => '28.10',
			'species' => 'mpu',
			'common_name' => 'Micromonas pusilla strain CCMP1545',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'TP19G02370' => array(
			'gene_id' => 'TP19G02370',
			'e_value' => '3e-17',
			'bit_score' => '83.2',
			'alignment_length' => '174',
			'identity_percentage' => '29.89',
			'species' => 'tps',
			'common_name' => 'Thalassiosira pseudonana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0289029' => array(
			'gene_id' => 'DDB_G0289029',
			'e_value' => '7e-17',
			'bit_score' => '85.5',
			'alignment_length' => '178',
			'identity_percentage' => '31.46',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ES0031G00390' => array(
			'gene_id' => 'ES0031G00390',
			'e_value' => '1e-16',
			'bit_score' => '85.5',
			'alignment_length' => '173',
			'identity_percentage' => '27.75',
			'species' => 'esi',
			'common_name' => 'Ectocarpus siliculosus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CV00G60260' => array(
			'gene_id' => 'CV00G60260',
			'e_value' => '1e-16',
			'bit_score' => '85.5',
			'alignment_length' => '173',
			'identity_percentage' => '30.64',
			'species' => 'cvu',
			'common_name' => 'Coccomyxa subellipsoidea C-169',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G52315' => array(
			'gene_id' => 'AT1G52315',
			'e_value' => '1e-16',
			'bit_score' => '84.3',
			'alignment_length' => '179',
			'identity_percentage' => '27.93',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'DDB_G0284389' => array(
			'gene_id' => 'DDB_G0284389',
			'e_value' => '7e-16',
			'bit_score' => '84.0',
			'alignment_length' => '172',
			'identity_percentage' => '30.23',
			'species' => 'ddi',
			'common_name' => 'Dictyostelium discoideum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS02G06430' => array(
			'gene_id' => 'OS02G06430',
			'e_value' => '2e-15',
			'bit_score' => '82.4',
			'alignment_length' => '180',
			'identity_percentage' => '27.22',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT4G32350' => array(
			'gene_id' => 'AT4G32350',
			'e_value' => '3e-15',
			'bit_score' => '81.6',
			'alignment_length' => '178',
			'identity_percentage' => '27.53',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OS06G47250' => array(
			'gene_id' => 'OS06G47250',
			'e_value' => '4e-15',
			'bit_score' => '81.6',
			'alignment_length' => '179',
			'identity_percentage' => '27.93',
			'species' => 'osa',
			'common_name' => 'Oryza sativa',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OM_09G01680' => array(
			'gene_id' => 'OM_09G01680',
			'e_value' => '9e-15',
			'bit_score' => '79.0',
			'alignment_length' => '181',
			'identity_percentage' => '27.62',
			'species' => 'ome',
			'common_name' => 'Ostreococcus mediterraneus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'PTI_05G04260' => array(
			'gene_id' => 'PTI_05G04260',
			'e_value' => '5e-14',
			'bit_score' => '76.6',
			'alignment_length' => '167',
			'identity_percentage' => '25.15',
			'species' => 'ptri',
			'common_name' => 'Phaeodactylum tricornutum',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'HE0000G04150' => array(
			'gene_id' => 'HE0000G04150',
			'e_value' => '2e-13',
			'bit_score' => '72.4',
			'alignment_length' => '125',
			'identity_percentage' => '28.00',
			'species' => 'hsp',
			'common_name' => 'Helicosporidium sp. ',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AA0002G00430' => array(
			'gene_id' => 'AA0002G00430',
			'e_value' => '3e-13',
			'bit_score' => '72.0',
			'alignment_length' => '168',
			'identity_percentage' => '29.17',
			'species' => 'aan',
			'common_name' => 'Aureococcus anophagefferens',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AP00G00640' => array(
			'gene_id' => 'AP00G00640',
			'e_value' => '5e-13',
			'bit_score' => '73.9',
			'alignment_length' => '199',
			'identity_percentage' => '29.15',
			'species' => 'apr',
			'common_name' => 'Auxenochlorella protothecoides',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G94970' => array(
			'gene_id' => 'AC00G94970',
			'e_value' => '2e-12',
			'bit_score' => '71.6',
			'alignment_length' => '180',
			'identity_percentage' => '26.11',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT3G15490' => array(
			'gene_id' => 'AT3G15490',
			'e_value' => '3e-12',
			'bit_score' => '69.3',
			'alignment_length' => '130',
			'identity_percentage' => '33.08',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AC00G94960' => array(
			'gene_id' => 'AC00G94960',
			'e_value' => '8e-12',
			'bit_score' => '68.6',
			'alignment_length' => '180',
			'identity_percentage' => '26.11',
			'species' => 'acg',
			'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'WBGene00010736' => array(
			'gene_id' => 'WBGene00010736',
			'e_value' => '2e-11',
			'bit_score' => '69.3',
			'alignment_length' => '174',
			'identity_percentage' => '26.44',
			'species' => 'cel',
			'common_name' => 'Caenorhabditis elegans',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ENSMUSG00000031729' => array(
			'gene_id' => 'ENSMUSG00000031729',
			'e_value' => '2e-11',
			'bit_score' => '68.9',
			'alignment_length' => '183',
			'identity_percentage' => '26.23',
			'species' => 'mus',
			'common_name' => 'Mus musculus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'OL03G01580' => array(
			'gene_id' => 'OL03G01580',
			'e_value' => '3e-11',
			'bit_score' => '68.2',
			'alignment_length' => '180',
			'identity_percentage' => '26.67',
			'species' => 'olu',
			'common_name' => 'Ostreococcus lucimarinus',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'FBgn0035715' => array(
			'gene_id' => 'FBgn0035715',
			'e_value' => '1e-09',
			'bit_score' => '63.5',
			'alignment_length' => '173',
			'identity_percentage' => '24.86',
			'species' => 'drm',
			'common_name' => 'Drosophila melanogaster',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'ORCC809_03G01460' => array(
			'gene_id' => 'ORCC809_03G01460',
			'e_value' => '3e-09',
			'bit_score' => '62.4',
			'alignment_length' => '175',
			'identity_percentage' => '29.14',
			'species' => 'orcc809',
			'common_name' => 'Ostreococcus sp RCC809',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'CNC64A_044G00100' => array(
			'gene_id' => 'CNC64A_044G00100',
			'e_value' => '2e-08',
			'bit_score' => '60.1',
			'alignment_length' => '192',
			'identity_percentage' => '23.96',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'BPRRCC1105_12G02820' => array(
			'gene_id' => 'BPRRCC1105_12G02820',
			'e_value' => '6e-08',
			'bit_score' => '58.2',
			'alignment_length' => '163',
			'identity_percentage' => '23.93',
			'species' => 'bprrcc1105',
			'common_name' => 'Bathycoccus prasinos',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'YNL265C' => array(
			'gene_id' => 'YNL265C',
			'e_value' => '3e-06',
			'bit_score' => '52.8',
			'alignment_length' => '173',
			'identity_percentage' => '26.01',
			'species' => 'sac',
			'common_name' => 'Saccharomyces cerevisiae strain S288C',
			'gf' => array(
				[maximum depth reached]
			)
		),
		'AT1G51900' => array(
			'gene_id' => 'AT1G51900',
			'e_value' => '7e-06',
			'bit_score' => '52.4',
			'alignment_length' => '188',
			'identity_percentage' => '25.00',
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'gf' => array(
				[maximum depth reached]
			)
		)
	),
	'similarity_hits_species' => array(
		'ath' => array(
			(int) 0 => 'AT1G13340',
			(int) 1 => 'AT4G35730',
			(int) 2 => 'AT2G19710',
			(int) 3 => 'AT1G25420',
			(int) 4 => 'AT1G34220',
			(int) 5 => 'AT4G29440',
			(int) 6 => 'AT2G14830',
			(int) 7 => 'AT1G79910',
			(int) 8 => 'AT1G52315',
			(int) 9 => 'AT4G32350',
			(int) 10 => 'AT3G15490',
			(int) 11 => 'AT1G51900'
		),
		'atr' => array(
			(int) 0 => 'ATR_00002G00640',
			(int) 1 => 'ATR_00036G01680',
			(int) 2 => 'ATR_00001G02660',
			(int) 3 => 'ATR_00079G00350',
			(int) 4 => 'ATR_00003G02620',
			(int) 5 => 'ATR_00200G00070',
			(int) 6 => 'ATR_00010G02880'
		),
		'osa' => array(
			(int) 0 => 'OS03G50210',
			(int) 1 => 'OS01G49350',
			(int) 2 => 'OS08G07830',
			(int) 3 => 'OS09G37510',
			(int) 4 => 'OS01G51010',
			(int) 5 => 'OS03G15230',
			(int) 6 => 'OS03G15210',
			(int) 7 => 'OS03G15220',
			(int) 8 => 'OS02G06430',
			(int) 9 => 'OS06G47250'
		),
		'ppa' => array(
			(int) 0 => 'PP00079G00210',
			(int) 1 => 'PP00030G00310',
			(int) 2 => 'PP00095G00370',
			(int) 3 => 'PP00043G00230'
		),
		'cre' => array(
			(int) 0 => 'CR10G03920'
		),
		'phs' => array(
			(int) 0 => 'phs256930'
		),
		'nga' => array(
			(int) 0 => 'Naga_100136g20'
		),
		'vca' => array(
			(int) 0 => 'VC00G64720'
		),
		'mpu' => array(
			(int) 0 => 'MP17G00050'
		),
		'tps' => array(
			(int) 0 => 'TP19G02370'
		),
		'ddi' => array(
			(int) 0 => 'DDB_G0289029',
			(int) 1 => 'DDB_G0284389'
		),
		'esi' => array(
			(int) 0 => 'ES0031G00390'
		),
		'cvu' => array(
			(int) 0 => 'CV00G60260'
		),
		'ome' => array(
			(int) 0 => 'OM_09G01680'
		),
		'ptri' => array(
			(int) 0 => 'PTI_05G04260'
		),
		'hsp' => array(
			(int) 0 => 'HE0000G04150'
		),
		'aan' => array(
			(int) 0 => 'AA0002G00430'
		),
		'apr' => array(
			(int) 0 => 'AP00G00640'
		),
		'acg' => array(
			(int) 0 => 'AC00G94970',
			(int) 1 => 'AC00G94960'
		),
		'cel' => array(
			(int) 0 => 'WBGene00010736'
		),
		'mus' => array(
			(int) 0 => 'ENSMUSG00000031729'
		),
		'olu' => array(
			(int) 0 => 'OL03G01580'
		),
		'drm' => array(
			(int) 0 => 'FBgn0035715'
		),
		'orcc809' => array(
			(int) 0 => 'ORCC809_03G01460'
		),
		'bprrcc1105' => array(
			(int) 0 => 'BPRRCC1105_12G02820'
		),
		'sac' => array(
			(int) 0 => 'YNL265C'
		)
	),
	'gene_id' => 'AT1G13340',
	'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' => 'AT1G13340',
	'data_type' => 'gene_id',
	'allow_async_use' => true,
	'gene_placeholder' => 'AC00G28340',
	'gf_placeholder' => 'HOM03P007610',
	'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(
	'AT1G13340' => array(
		'gene_id' => 'AT1G13340',
		'e_value' => '0.0',
		'bit_score' => '840',
		'alignment_length' => '410',
		'identity_percentage' => '100.00',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P042457'
		)
	),
	'ATR_00002G00640' => array(
		'gene_id' => 'ATR_00002G00640',
		'e_value' => '1e-55',
		'bit_score' => '198',
		'alignment_length' => '186',
		'identity_percentage' => '49.46',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P042457'
		)
	),
	'OS03G50210' => array(
		'gene_id' => 'OS03G50210',
		'e_value' => '5e-47',
		'bit_score' => '170',
		'alignment_length' => '183',
		'identity_percentage' => '46.99',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P042457'
		)
	),
	'PP00079G00210' => array(
		'gene_id' => 'PP00079G00210',
		'e_value' => '9e-40',
		'bit_score' => '154',
		'alignment_length' => '192',
		'identity_percentage' => '39.58',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'PP00030G00310' => array(
		'gene_id' => 'PP00030G00310',
		'e_value' => '4e-39',
		'bit_score' => '152',
		'alignment_length' => '190',
		'identity_percentage' => '37.89',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ATR_00036G01680' => array(
		'gene_id' => 'ATR_00036G01680',
		'e_value' => '2e-31',
		'bit_score' => '132',
		'alignment_length' => '175',
		'identity_percentage' => '36.00',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'OS01G49350' => array(
		'gene_id' => 'OS01G49350',
		'e_value' => '7e-31',
		'bit_score' => '125',
		'alignment_length' => '194',
		'identity_percentage' => '32.47',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P039350'
		)
	),
	'OS08G07830' => array(
		'gene_id' => 'OS08G07830',
		'e_value' => '8e-31',
		'bit_score' => '127',
		'alignment_length' => '176',
		'identity_percentage' => '35.80',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT4G35730' => array(
		'gene_id' => 'AT4G35730',
		'e_value' => '1e-29',
		'bit_score' => '123',
		'alignment_length' => '188',
		'identity_percentage' => '33.51',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P066330'
		)
	),
	'ATR_00001G02660' => array(
		'gene_id' => 'ATR_00001G02660',
		'e_value' => '2e-29',
		'bit_score' => '125',
		'alignment_length' => '167',
		'identity_percentage' => '36.53',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P010073'
		)
	),
	'PP00095G00370' => array(
		'gene_id' => 'PP00095G00370',
		'e_value' => '3e-29',
		'bit_score' => '125',
		'alignment_length' => '180',
		'identity_percentage' => '33.89',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P087707'
		)
	),
	'AT2G19710' => array(
		'gene_id' => 'AT2G19710',
		'e_value' => '9e-29',
		'bit_score' => '123',
		'alignment_length' => '181',
		'identity_percentage' => '34.81',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P049438'
		)
	),
	'AT1G25420' => array(
		'gene_id' => 'AT1G25420',
		'e_value' => '3e-28',
		'bit_score' => '117',
		'alignment_length' => '190',
		'identity_percentage' => '33.16',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P039350'
		)
	),
	'OS09G37510' => array(
		'gene_id' => 'OS09G37510',
		'e_value' => '9e-28',
		'bit_score' => '117',
		'alignment_length' => '171',
		'identity_percentage' => '33.92',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P066330'
		)
	),
	'ATR_00079G00350' => array(
		'gene_id' => 'ATR_00079G00350',
		'e_value' => '4e-27',
		'bit_score' => '114',
		'alignment_length' => '149',
		'identity_percentage' => '36.91',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P039350'
		)
	),
	'OS01G51010' => array(
		'gene_id' => 'OS01G51010',
		'e_value' => '4e-27',
		'bit_score' => '118',
		'alignment_length' => '179',
		'identity_percentage' => '31.84',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'OS03G15230' => array(
		'gene_id' => 'OS03G15230',
		'e_value' => '2e-26',
		'bit_score' => '115',
		'alignment_length' => '230',
		'identity_percentage' => '32.61',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P034414'
		)
	),
	'AT1G34220' => array(
		'gene_id' => 'AT1G34220',
		'e_value' => '2e-25',
		'bit_score' => '112',
		'alignment_length' => '220',
		'identity_percentage' => '29.09',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT4G29440' => array(
		'gene_id' => 'AT4G29440',
		'e_value' => '6e-25',
		'bit_score' => '111',
		'alignment_length' => '180',
		'identity_percentage' => '31.67',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P049438'
		)
	),
	'OS03G15210' => array(
		'gene_id' => 'OS03G15210',
		'e_value' => '2e-24',
		'bit_score' => '103',
		'alignment_length' => '174',
		'identity_percentage' => '35.06',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P034414'
		)
	),
	'OS03G15220' => array(
		'gene_id' => 'OS03G15220',
		'e_value' => '9e-23',
		'bit_score' => '99.0',
		'alignment_length' => '174',
		'identity_percentage' => '33.91',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P034414'
		)
	),
	'ATR_00003G02620' => array(
		'gene_id' => 'ATR_00003G02620',
		'e_value' => '1e-21',
		'bit_score' => '101',
		'alignment_length' => '171',
		'identity_percentage' => '32.16',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P183665'
		)
	),
	'CR10G03920' => array(
		'gene_id' => 'CR10G03920',
		'e_value' => '1e-21',
		'bit_score' => '100',
		'alignment_length' => '219',
		'identity_percentage' => '27.85',
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT2G14830' => array(
		'gene_id' => 'AT2G14830',
		'e_value' => '6e-21',
		'bit_score' => '97.8',
		'alignment_length' => '173',
		'identity_percentage' => '31.21',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P051073'
		)
	),
	'AT1G79910' => array(
		'gene_id' => 'AT1G79910',
		'e_value' => '7e-21',
		'bit_score' => '97.1',
		'alignment_length' => '178',
		'identity_percentage' => '28.65',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P075682'
		)
	),
	'phs256930' => array(
		'gene_id' => 'phs256930',
		'e_value' => '8e-21',
		'bit_score' => '95.9',
		'alignment_length' => '181',
		'identity_percentage' => '34.25',
		'species' => 'phs',
		'common_name' => 'Phytophtora sojae',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ATR_00200G00070' => array(
		'gene_id' => 'ATR_00200G00070',
		'e_value' => '1e-20',
		'bit_score' => '98.2',
		'alignment_length' => '175',
		'identity_percentage' => '33.14',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P075682'
		)
	),
	'ATR_00010G02880' => array(
		'gene_id' => 'ATR_00010G02880',
		'e_value' => '3e-20',
		'bit_score' => '96.7',
		'alignment_length' => '148',
		'identity_percentage' => '34.46',
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P206020'
		)
	),
	'Naga_100136g20' => array(
		'gene_id' => 'Naga_100136g20',
		'e_value' => '9e-20',
		'bit_score' => '92.4',
		'alignment_length' => '212',
		'identity_percentage' => '27.83',
		'species' => 'nga',
		'common_name' => 'Nannochloropsis gaditana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'PP00043G00230' => array(
		'gene_id' => 'PP00043G00230',
		'e_value' => '2e-18',
		'bit_score' => '91.7',
		'alignment_length' => '174',
		'identity_percentage' => '25.86',
		'species' => 'ppa',
		'common_name' => 'Physcomitrella patens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P158453'
		)
	),
	'VC00G64720' => array(
		'gene_id' => 'VC00G64720',
		'e_value' => '3e-18',
		'bit_score' => '90.5',
		'alignment_length' => '185',
		'identity_percentage' => '29.19',
		'species' => 'vca',
		'common_name' => 'Volvox carteri',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'MP17G00050' => array(
		'gene_id' => 'MP17G00050',
		'e_value' => '8e-18',
		'bit_score' => '88.6',
		'alignment_length' => '210',
		'identity_percentage' => '28.10',
		'species' => 'mpu',
		'common_name' => 'Micromonas pusilla strain CCMP1545',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'TP19G02370' => array(
		'gene_id' => 'TP19G02370',
		'e_value' => '3e-17',
		'bit_score' => '83.2',
		'alignment_length' => '174',
		'identity_percentage' => '29.89',
		'species' => 'tps',
		'common_name' => 'Thalassiosira pseudonana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'DDB_G0289029' => array(
		'gene_id' => 'DDB_G0289029',
		'e_value' => '7e-17',
		'bit_score' => '85.5',
		'alignment_length' => '178',
		'identity_percentage' => '31.46',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ES0031G00390' => array(
		'gene_id' => 'ES0031G00390',
		'e_value' => '1e-16',
		'bit_score' => '85.5',
		'alignment_length' => '173',
		'identity_percentage' => '27.75',
		'species' => 'esi',
		'common_name' => 'Ectocarpus siliculosus',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'CV00G60260' => array(
		'gene_id' => 'CV00G60260',
		'e_value' => '1e-16',
		'bit_score' => '85.5',
		'alignment_length' => '173',
		'identity_percentage' => '30.64',
		'species' => 'cvu',
		'common_name' => 'Coccomyxa subellipsoidea C-169',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT1G52315' => array(
		'gene_id' => 'AT1G52315',
		'e_value' => '1e-16',
		'bit_score' => '84.3',
		'alignment_length' => '179',
		'identity_percentage' => '27.93',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P116121'
		)
	),
	'DDB_G0284389' => array(
		'gene_id' => 'DDB_G0284389',
		'e_value' => '7e-16',
		'bit_score' => '84.0',
		'alignment_length' => '172',
		'identity_percentage' => '30.23',
		'species' => 'ddi',
		'common_name' => 'Dictyostelium discoideum',
		'gf' => array(
			'HOMFAM' => 'HOM03P000055',
			'ORTHOFAM' => 'ORTHO03P103792'
		)
	),
	'OS02G06430' => array(
		'gene_id' => 'OS02G06430',
		'e_value' => '2e-15',
		'bit_score' => '82.4',
		'alignment_length' => '180',
		'identity_percentage' => '27.22',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P049023'
		)
	),
	'AT4G32350' => array(
		'gene_id' => 'AT4G32350',
		'e_value' => '3e-15',
		'bit_score' => '81.6',
		'alignment_length' => '178',
		'identity_percentage' => '27.53',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P095477'
		)
	),
	'OS06G47250' => array(
		'gene_id' => 'OS06G47250',
		'e_value' => '4e-15',
		'bit_score' => '81.6',
		'alignment_length' => '179',
		'identity_percentage' => '27.93',
		'species' => 'osa',
		'common_name' => 'Oryza sativa',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P049023'
		)
	),
	'OM_09G01680' => array(
		'gene_id' => 'OM_09G01680',
		'e_value' => '9e-15',
		'bit_score' => '79.0',
		'alignment_length' => '181',
		'identity_percentage' => '27.62',
		'species' => 'ome',
		'common_name' => 'Ostreococcus mediterraneus',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'PTI_05G04260' => array(
		'gene_id' => 'PTI_05G04260',
		'e_value' => '5e-14',
		'bit_score' => '76.6',
		'alignment_length' => '167',
		'identity_percentage' => '25.15',
		'species' => 'ptri',
		'common_name' => 'Phaeodactylum tricornutum',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'HE0000G04150' => array(
		'gene_id' => 'HE0000G04150',
		'e_value' => '2e-13',
		'bit_score' => '72.4',
		'alignment_length' => '125',
		'identity_percentage' => '28.00',
		'species' => 'hsp',
		'common_name' => 'Helicosporidium sp. ',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AA0002G00430' => array(
		'gene_id' => 'AA0002G00430',
		'e_value' => '3e-13',
		'bit_score' => '72.0',
		'alignment_length' => '168',
		'identity_percentage' => '29.17',
		'species' => 'aan',
		'common_name' => 'Aureococcus anophagefferens',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AP00G00640' => array(
		'gene_id' => 'AP00G00640',
		'e_value' => '5e-13',
		'bit_score' => '73.9',
		'alignment_length' => '199',
		'identity_percentage' => '29.15',
		'species' => 'apr',
		'common_name' => 'Auxenochlorella protothecoides',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AC00G94970' => array(
		'gene_id' => 'AC00G94970',
		'e_value' => '2e-12',
		'bit_score' => '71.6',
		'alignment_length' => '180',
		'identity_percentage' => '26.11',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT3G15490' => array(
		'gene_id' => 'AT3G15490',
		'e_value' => '3e-12',
		'bit_score' => '69.3',
		'alignment_length' => '130',
		'identity_percentage' => '33.08',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P175619'
		)
	),
	'AC00G94960' => array(
		'gene_id' => 'AC00G94960',
		'e_value' => '8e-12',
		'bit_score' => '68.6',
		'alignment_length' => '180',
		'identity_percentage' => '26.11',
		'species' => 'acg',
		'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'WBGene00010736' => array(
		'gene_id' => 'WBGene00010736',
		'e_value' => '2e-11',
		'bit_score' => '69.3',
		'alignment_length' => '174',
		'identity_percentage' => '26.44',
		'species' => 'cel',
		'common_name' => 'Caenorhabditis elegans',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ENSMUSG00000031729' => array(
		'gene_id' => 'ENSMUSG00000031729',
		'e_value' => '2e-11',
		'bit_score' => '68.9',
		'alignment_length' => '183',
		'identity_percentage' => '26.23',
		'species' => 'mus',
		'common_name' => 'Mus musculus',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'OL03G01580' => array(
		'gene_id' => 'OL03G01580',
		'e_value' => '3e-11',
		'bit_score' => '68.2',
		'alignment_length' => '180',
		'identity_percentage' => '26.67',
		'species' => 'olu',
		'common_name' => 'Ostreococcus lucimarinus',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'FBgn0035715' => array(
		'gene_id' => 'FBgn0035715',
		'e_value' => '1e-09',
		'bit_score' => '63.5',
		'alignment_length' => '173',
		'identity_percentage' => '24.86',
		'species' => 'drm',
		'common_name' => 'Drosophila melanogaster',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'ORCC809_03G01460' => array(
		'gene_id' => 'ORCC809_03G01460',
		'e_value' => '3e-09',
		'bit_score' => '62.4',
		'alignment_length' => '175',
		'identity_percentage' => '29.14',
		'species' => 'orcc809',
		'common_name' => 'Ostreococcus sp RCC809',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'CNC64A_044G00100' => array(
		'gene_id' => 'CNC64A_044G00100',
		'e_value' => '2e-08',
		'bit_score' => '60.1',
		'alignment_length' => '192',
		'identity_percentage' => '23.96',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'BPRRCC1105_12G02820' => array(
		'gene_id' => 'BPRRCC1105_12G02820',
		'e_value' => '6e-08',
		'bit_score' => '58.2',
		'alignment_length' => '163',
		'identity_percentage' => '23.93',
		'species' => 'bprrcc1105',
		'common_name' => 'Bathycoccus prasinos',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'YNL265C' => array(
		'gene_id' => 'YNL265C',
		'e_value' => '3e-06',
		'bit_score' => '52.8',
		'alignment_length' => '173',
		'identity_percentage' => '26.01',
		'species' => 'sac',
		'common_name' => 'Saccharomyces cerevisiae strain S288C',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P001894'
		)
	),
	'AT1G51900' => array(
		'gene_id' => 'AT1G51900',
		'e_value' => '7e-06',
		'bit_score' => '52.4',
		'alignment_length' => '188',
		'identity_percentage' => '25.00',
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'gf' => array(
			'HOMFAM' => 'HOM03P000893',
			'ORTHOFAM' => 'ORTHO03P051073'
		)
	)
)
$similarity_hits_species = array(
	'ath' => array(
		(int) 0 => 'AT1G13340',
		(int) 1 => 'AT4G35730',
		(int) 2 => 'AT2G19710',
		(int) 3 => 'AT1G25420',
		(int) 4 => 'AT1G34220',
		(int) 5 => 'AT4G29440',
		(int) 6 => 'AT2G14830',
		(int) 7 => 'AT1G79910',
		(int) 8 => 'AT1G52315',
		(int) 9 => 'AT4G32350',
		(int) 10 => 'AT3G15490',
		(int) 11 => 'AT1G51900'
	),
	'atr' => array(
		(int) 0 => 'ATR_00002G00640',
		(int) 1 => 'ATR_00036G01680',
		(int) 2 => 'ATR_00001G02660',
		(int) 3 => 'ATR_00079G00350',
		(int) 4 => 'ATR_00003G02620',
		(int) 5 => 'ATR_00200G00070',
		(int) 6 => 'ATR_00010G02880'
	),
	'osa' => array(
		(int) 0 => 'OS03G50210',
		(int) 1 => 'OS01G49350',
		(int) 2 => 'OS08G07830',
		(int) 3 => 'OS09G37510',
		(int) 4 => 'OS01G51010',
		(int) 5 => 'OS03G15230',
		(int) 6 => 'OS03G15210',
		(int) 7 => 'OS03G15220',
		(int) 8 => 'OS02G06430',
		(int) 9 => 'OS06G47250'
	),
	'ppa' => array(
		(int) 0 => 'PP00079G00210',
		(int) 1 => 'PP00030G00310',
		(int) 2 => 'PP00095G00370',
		(int) 3 => 'PP00043G00230'
	),
	'cre' => array(
		(int) 0 => 'CR10G03920'
	),
	'phs' => array(
		(int) 0 => 'phs256930'
	),
	'nga' => array(
		(int) 0 => 'Naga_100136g20'
	),
	'vca' => array(
		(int) 0 => 'VC00G64720'
	),
	'mpu' => array(
		(int) 0 => 'MP17G00050'
	),
	'tps' => array(
		(int) 0 => 'TP19G02370'
	),
	'ddi' => array(
		(int) 0 => 'DDB_G0289029',
		(int) 1 => 'DDB_G0284389'
	),
	'esi' => array(
		(int) 0 => 'ES0031G00390'
	),
	'cvu' => array(
		(int) 0 => 'CV00G60260'
	),
	'ome' => array(
		(int) 0 => 'OM_09G01680'
	),
	'ptri' => array(
		(int) 0 => 'PTI_05G04260'
	),
	'hsp' => array(
		(int) 0 => 'HE0000G04150'
	),
	'aan' => array(
		(int) 0 => 'AA0002G00430'
	),
	'apr' => array(
		(int) 0 => 'AP00G00640'
	),
	'acg' => array(
		(int) 0 => 'AC00G94970',
		(int) 1 => 'AC00G94960'
	),
	'cel' => array(
		(int) 0 => 'WBGene00010736'
	),
	'mus' => array(
		(int) 0 => 'ENSMUSG00000031729'
	),
	'olu' => array(
		(int) 0 => 'OL03G01580'
	),
	'drm' => array(
		(int) 0 => 'FBgn0035715'
	),
	'orcc809' => array(
		(int) 0 => 'ORCC809_03G01460'
	),
	'bprrcc1105' => array(
		(int) 0 => 'BPRRCC1105_12G02820'
	),
	'sac' => array(
		(int) 0 => 'YNL265C'
	)
)
$gene_id = 'AT1G13340'
$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 = 'AT1G13340'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'AC00G28340'
$gf_placeholder = 'HOM03P007610'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
	'gene_id' => 'CNC64A_044G00100',
	'e_value' => '2e-08',
	'bit_score' => '60.1',
	'alignment_length' => '192',
	'identity_percentage' => '23.96',
	'gf' => array(
		'HOMFAM' => 'HOM03P000893',
		'ORTHOFAM' => 'ORTHO03P001894'
	)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00100'
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