|
CNC64A_044G00080 |
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(
'OL02G04740' => array(
'gene_id' => 'OL02G04740',
'e_value' => '9e-63',
'bit_score' => '191',
'alignment_length' => '91',
'identity_percentage' => '100.00',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'OT_02G01350' => array(
'gene_id' => 'OT_02G01350',
'e_value' => '2e-35',
'bit_score' => '126',
'alignment_length' => '93',
'identity_percentage' => '64.52',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'BPRRCC1105_14G03340' => array(
'gene_id' => 'BPRRCC1105_14G03340',
'e_value' => '3e-22',
'bit_score' => '90.9',
'alignment_length' => '89',
'identity_percentage' => '47.19',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
[maximum depth reached]
)
),
'PTI_22G00250' => array(
'gene_id' => 'PTI_22G00250',
'e_value' => '3e-20',
'bit_score' => '88.6',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000028233' => array(
'gene_id' => 'ENSMUSG00000028233',
'e_value' => '9e-20',
'bit_score' => '88.2',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000093862' => array(
'gene_id' => 'ENSMUSG00000093862',
'e_value' => '1e-19',
'bit_score' => '87.4',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'emh729020' => array(
'gene_id' => 'emh729020',
'e_value' => '2e-19',
'bit_score' => '84.7',
'alignment_length' => '89',
'identity_percentage' => '47.19',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_02G02560' => array(
'gene_id' => 'ORCC809_02G02560',
'e_value' => '9e-19',
'bit_score' => '79.0',
'alignment_length' => '82',
'identity_percentage' => '50.00',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'AC00G95840' => array(
'gene_id' => 'AC00G95840',
'e_value' => '1e-18',
'bit_score' => '80.9',
'alignment_length' => '91',
'identity_percentage' => '45.05',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'AT1G30550' => array(
'gene_id' => 'AT1G30550',
'e_value' => '3e-18',
'bit_score' => '82.8',
'alignment_length' => '91',
'identity_percentage' => '49.45',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AA0018G01160' => array(
'gene_id' => 'AA0018G01160',
'e_value' => '2e-17',
'bit_score' => '75.9',
'alignment_length' => '89',
'identity_percentage' => '46.07',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'TP02G08210' => array(
'gene_id' => 'TP02G08210',
'e_value' => '3e-17',
'bit_score' => '78.2',
'alignment_length' => '93',
'identity_percentage' => '43.01',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.19g00730' => array(
'gene_id' => 'RCC4223.19g00730',
'e_value' => '5e-17',
'bit_score' => '79.3',
'alignment_length' => '84',
'identity_percentage' => '50.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'FBgn0266195' => array(
'gene_id' => 'FBgn0266195',
'e_value' => '9e-17',
'bit_score' => '78.6',
'alignment_length' => '91',
'identity_percentage' => '45.05',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
[maximum depth reached]
)
),
'AT1G45231' => array(
'gene_id' => 'AT1G45231',
'e_value' => '1e-16',
'bit_score' => '78.2',
'alignment_length' => '91',
'identity_percentage' => '43.96',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_044G00080' => array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-16',
'bit_score' => '77.0',
'alignment_length' => '93',
'identity_percentage' => '44.09',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00003G02210' => array(
'gene_id' => 'ATR_00003G02210',
'e_value' => '2e-16',
'bit_score' => '78.2',
'alignment_length' => '90',
'identity_percentage' => '41.11',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'SPAC2G11.15c' => array(
'gene_id' => 'SPAC2G11.15c',
'e_value' => '2e-16',
'bit_score' => '75.5',
'alignment_length' => '91',
'identity_percentage' => '42.86',
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'gf' => array(
[maximum depth reached]
)
),
'PI00G01490' => array(
'gene_id' => 'PI00G01490',
'e_value' => '2e-16',
'bit_score' => '77.8',
'alignment_length' => '88',
'identity_percentage' => '47.73',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'MP02G06160' => array(
'gene_id' => 'MP02G06160',
'e_value' => '3e-16',
'bit_score' => '75.9',
'alignment_length' => '110',
'identity_percentage' => '40.91',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'PP00092G00090' => array(
'gene_id' => 'PP00092G00090',
'e_value' => '3e-16',
'bit_score' => '77.8',
'alignment_length' => '89',
'identity_percentage' => '44.94',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0288547' => array(
'gene_id' => 'DDB_G0288547',
'e_value' => '5e-16',
'bit_score' => '75.1',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'OM_04G01940' => array(
'gene_id' => 'OM_04G01940',
'e_value' => '1e-15',
'bit_score' => '73.9',
'alignment_length' => '95',
'identity_percentage' => '42.11',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'phs121750' => array(
'gene_id' => 'phs121750',
'e_value' => '6e-15',
'bit_score' => '73.2',
'alignment_length' => '90',
'identity_percentage' => '43.33',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00019G00550' => array(
'gene_id' => 'ATR_00019G00550',
'e_value' => '6e-15',
'bit_score' => '72.0',
'alignment_length' => '89',
'identity_percentage' => '42.70',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'ES0120G00110' => array(
'gene_id' => 'ES0120G00110',
'e_value' => '7e-15',
'bit_score' => '73.6',
'alignment_length' => '90',
'identity_percentage' => '44.44',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_01G06910' => array(
'gene_id' => 'MRCC299_01G06910',
'e_value' => '1e-14',
'bit_score' => '72.8',
'alignment_length' => '104',
'identity_percentage' => '41.35',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'OS03G27930' => array(
'gene_id' => 'OS03G27930',
'e_value' => '1e-14',
'bit_score' => '73.2',
'alignment_length' => '89',
'identity_percentage' => '41.57',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'WBGene00011631' => array(
'gene_id' => 'WBGene00011631',
'e_value' => '3e-14',
'bit_score' => '71.6',
'alignment_length' => '90',
'identity_percentage' => '45.56',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100003g58' => array(
'gene_id' => 'Naga_100003g58',
'e_value' => '3e-14',
'bit_score' => '71.2',
'alignment_length' => '89',
'identity_percentage' => '46.07',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'ccr132780' => array(
'gene_id' => 'ccr132780',
'e_value' => '3e-14',
'bit_score' => '69.3',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
[maximum depth reached]
)
),
'FC004G05310' => array(
'gene_id' => 'FC004G05310',
'e_value' => '6e-14',
'bit_score' => '68.6',
'alignment_length' => '91',
'identity_percentage' => '42.86',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'PTI_22G00920' => array(
'gene_id' => 'PTI_22G00920',
'e_value' => '7e-14',
'bit_score' => '69.7',
'alignment_length' => '89',
'identity_percentage' => '44.94',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'OS06G08800' => array(
'gene_id' => 'OS06G08800',
'e_value' => '2e-13',
'bit_score' => '67.8',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'CR06G11280' => array(
'gene_id' => 'CR06G11280',
'e_value' => '5e-13',
'bit_score' => '68.9',
'alignment_length' => '96',
'identity_percentage' => '41.67',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'CV00G61210' => array(
'gene_id' => 'CV00G61210',
'e_value' => '5e-13',
'bit_score' => '65.5',
'alignment_length' => '83',
'identity_percentage' => '38.55',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'TP07G02910' => array(
'gene_id' => 'TP07G02910',
'e_value' => '6e-13',
'bit_score' => '64.7',
'alignment_length' => '108',
'identity_percentage' => '38.89',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'AP00G00630' => array(
'gene_id' => 'AP00G00630',
'e_value' => '1e-12',
'bit_score' => '67.0',
'alignment_length' => '67',
'identity_percentage' => '47.76',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'FC009G01340' => array(
'gene_id' => 'FC009G01340',
'e_value' => '2e-11',
'bit_score' => '61.6',
'alignment_length' => '91',
'identity_percentage' => '38.46',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'gsu74830' => array(
'gene_id' => 'gsu74830',
'e_value' => '2e-09',
'bit_score' => '55.8',
'alignment_length' => '88',
'identity_percentage' => '39.77',
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'gf' => array(
[maximum depth reached]
)
),
'pte492450' => array(
'gene_id' => 'pte492450',
'e_value' => '6e-09',
'bit_score' => '55.1',
'alignment_length' => '85',
'identity_percentage' => '35.29',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'pte317770' => array(
'gene_id' => 'pte317770',
'e_value' => '1e-08',
'bit_score' => '54.3',
'alignment_length' => '92',
'identity_percentage' => '32.61',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'YPL157W' => array(
'gene_id' => 'YPL157W',
'e_value' => '3e-07',
'bit_score' => '50.4',
'alignment_length' => '90',
'identity_percentage' => '36.67',
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'olu' => array(
(int) 0 => 'OL02G04740'
),
'ota' => array(
(int) 0 => 'OT_02G01350'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_14G03340'
),
'ptri' => array(
(int) 0 => 'PTI_22G00250',
(int) 1 => 'PTI_22G00920'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000028233',
(int) 1 => 'ENSMUSG00000093862'
),
'emh' => array(
(int) 0 => 'emh729020'
),
'orcc809' => array(
(int) 0 => 'ORCC809_02G02560'
),
'acg' => array(
(int) 0 => 'AC00G95840'
),
'ath' => array(
(int) 0 => 'AT1G30550',
(int) 1 => 'AT1G45231'
),
'aan' => array(
(int) 0 => 'AA0018G01160'
),
'tps' => array(
(int) 0 => 'TP02G08210',
(int) 1 => 'TP07G02910'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.19g00730'
),
'drm' => array(
(int) 0 => 'FBgn0266195'
),
'atr' => array(
(int) 0 => 'ATR_00003G02210',
(int) 1 => 'ATR_00019G00550'
),
'scp' => array(
(int) 0 => 'SPAC2G11.15c'
),
'pse3' => array(
(int) 0 => 'PI00G01490'
),
'mpu' => array(
(int) 0 => 'MP02G06160'
),
'ppa' => array(
(int) 0 => 'PP00092G00090'
),
'ddi' => array(
(int) 0 => 'DDB_G0288547'
),
'ome' => array(
(int) 0 => 'OM_04G01940'
),
'phs' => array(
(int) 0 => 'phs121750'
),
'esi' => array(
(int) 0 => 'ES0120G00110'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_01G06910'
),
'osa' => array(
(int) 0 => 'OS03G27930',
(int) 1 => 'OS06G08800'
),
'cel' => array(
(int) 0 => 'WBGene00011631'
),
'nga' => array(
(int) 0 => 'Naga_100003g58'
),
'ccr' => array(
(int) 0 => 'ccr132780'
),
'fcy' => array(
(int) 0 => 'FC004G05310',
(int) 1 => 'FC009G01340'
),
'cre' => array(
(int) 0 => 'CR06G11280'
),
'cvu' => array(
(int) 0 => 'CV00G61210'
),
'apr' => array(
(int) 0 => 'AP00G00630'
),
'gsu' => array(
(int) 0 => 'gsu74830'
),
'pte' => array(
(int) 0 => 'pte492450',
(int) 1 => 'pte317770'
),
'sac' => array(
(int) 0 => 'YPL157W'
)
),
'gene_id' => 'OL02G04740',
'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' => 'OL02G04740',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'OM_SOC01G00190',
'gf_placeholder' => 'HOM03P007387',
'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(
'OL02G04740' => array(
'gene_id' => 'OL02G04740',
'e_value' => '9e-63',
'bit_score' => '191',
'alignment_length' => '91',
'identity_percentage' => '100.00',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OT_02G01350' => array(
'gene_id' => 'OT_02G01350',
'e_value' => '2e-35',
'bit_score' => '126',
'alignment_length' => '93',
'identity_percentage' => '64.52',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'BPRRCC1105_14G03340' => array(
'gene_id' => 'BPRRCC1105_14G03340',
'e_value' => '3e-22',
'bit_score' => '90.9',
'alignment_length' => '89',
'identity_percentage' => '47.19',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PTI_22G00250' => array(
'gene_id' => 'PTI_22G00250',
'e_value' => '3e-20',
'bit_score' => '88.6',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P064266'
)
),
'ENSMUSG00000028233' => array(
'gene_id' => 'ENSMUSG00000028233',
'e_value' => '9e-20',
'bit_score' => '88.2',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ENSMUSG00000093862' => array(
'gene_id' => 'ENSMUSG00000093862',
'e_value' => '1e-19',
'bit_score' => '87.4',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'emh729020' => array(
'gene_id' => 'emh729020',
'e_value' => '2e-19',
'bit_score' => '84.7',
'alignment_length' => '89',
'identity_percentage' => '47.19',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ORCC809_02G02560' => array(
'gene_id' => 'ORCC809_02G02560',
'e_value' => '9e-19',
'bit_score' => '79.0',
'alignment_length' => '82',
'identity_percentage' => '50.00',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AC00G95840' => array(
'gene_id' => 'AC00G95840',
'e_value' => '1e-18',
'bit_score' => '80.9',
'alignment_length' => '91',
'identity_percentage' => '45.05',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AT1G30550' => array(
'gene_id' => 'AT1G30550',
'e_value' => '3e-18',
'bit_score' => '82.8',
'alignment_length' => '91',
'identity_percentage' => '49.45',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AA0018G01160' => array(
'gene_id' => 'AA0018G01160',
'e_value' => '2e-17',
'bit_score' => '75.9',
'alignment_length' => '89',
'identity_percentage' => '46.07',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'TP02G08210' => array(
'gene_id' => 'TP02G08210',
'e_value' => '3e-17',
'bit_score' => '78.2',
'alignment_length' => '93',
'identity_percentage' => '43.01',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'RCC4223.19g00730' => array(
'gene_id' => 'RCC4223.19g00730',
'e_value' => '5e-17',
'bit_score' => '79.3',
'alignment_length' => '84',
'identity_percentage' => '50.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FBgn0266195' => array(
'gene_id' => 'FBgn0266195',
'e_value' => '9e-17',
'bit_score' => '78.6',
'alignment_length' => '91',
'identity_percentage' => '45.05',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AT1G45231' => array(
'gene_id' => 'AT1G45231',
'e_value' => '1e-16',
'bit_score' => '78.2',
'alignment_length' => '91',
'identity_percentage' => '43.96',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CNC64A_044G00080' => array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-16',
'bit_score' => '77.0',
'alignment_length' => '93',
'identity_percentage' => '44.09',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ATR_00003G02210' => array(
'gene_id' => 'ATR_00003G02210',
'e_value' => '2e-16',
'bit_score' => '78.2',
'alignment_length' => '90',
'identity_percentage' => '41.11',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'SPAC2G11.15c' => array(
'gene_id' => 'SPAC2G11.15c',
'e_value' => '2e-16',
'bit_score' => '75.5',
'alignment_length' => '91',
'identity_percentage' => '42.86',
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PI00G01490' => array(
'gene_id' => 'PI00G01490',
'e_value' => '2e-16',
'bit_score' => '77.8',
'alignment_length' => '88',
'identity_percentage' => '47.73',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'MP02G06160' => array(
'gene_id' => 'MP02G06160',
'e_value' => '3e-16',
'bit_score' => '75.9',
'alignment_length' => '110',
'identity_percentage' => '40.91',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PP00092G00090' => array(
'gene_id' => 'PP00092G00090',
'e_value' => '3e-16',
'bit_score' => '77.8',
'alignment_length' => '89',
'identity_percentage' => '44.94',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'DDB_G0288547' => array(
'gene_id' => 'DDB_G0288547',
'e_value' => '5e-16',
'bit_score' => '75.1',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OM_04G01940' => array(
'gene_id' => 'OM_04G01940',
'e_value' => '1e-15',
'bit_score' => '73.9',
'alignment_length' => '95',
'identity_percentage' => '42.11',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'phs121750' => array(
'gene_id' => 'phs121750',
'e_value' => '6e-15',
'bit_score' => '73.2',
'alignment_length' => '90',
'identity_percentage' => '43.33',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ATR_00019G00550' => array(
'gene_id' => 'ATR_00019G00550',
'e_value' => '6e-15',
'bit_score' => '72.0',
'alignment_length' => '89',
'identity_percentage' => '42.70',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ES0120G00110' => array(
'gene_id' => 'ES0120G00110',
'e_value' => '7e-15',
'bit_score' => '73.6',
'alignment_length' => '90',
'identity_percentage' => '44.44',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'MRCC299_01G06910' => array(
'gene_id' => 'MRCC299_01G06910',
'e_value' => '1e-14',
'bit_score' => '72.8',
'alignment_length' => '104',
'identity_percentage' => '41.35',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OS03G27930' => array(
'gene_id' => 'OS03G27930',
'e_value' => '1e-14',
'bit_score' => '73.2',
'alignment_length' => '89',
'identity_percentage' => '41.57',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'WBGene00011631' => array(
'gene_id' => 'WBGene00011631',
'e_value' => '3e-14',
'bit_score' => '71.6',
'alignment_length' => '90',
'identity_percentage' => '45.56',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'Naga_100003g58' => array(
'gene_id' => 'Naga_100003g58',
'e_value' => '3e-14',
'bit_score' => '71.2',
'alignment_length' => '89',
'identity_percentage' => '46.07',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ccr132780' => array(
'gene_id' => 'ccr132780',
'e_value' => '3e-14',
'bit_score' => '69.3',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FC004G05310' => array(
'gene_id' => 'FC004G05310',
'e_value' => '6e-14',
'bit_score' => '68.6',
'alignment_length' => '91',
'identity_percentage' => '42.86',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P064266'
)
),
'PTI_22G00920' => array(
'gene_id' => 'PTI_22G00920',
'e_value' => '7e-14',
'bit_score' => '69.7',
'alignment_length' => '89',
'identity_percentage' => '44.94',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OS06G08800' => array(
'gene_id' => 'OS06G08800',
'e_value' => '2e-13',
'bit_score' => '67.8',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CR06G11280' => array(
'gene_id' => 'CR06G11280',
'e_value' => '5e-13',
'bit_score' => '68.9',
'alignment_length' => '96',
'identity_percentage' => '41.67',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CV00G61210' => array(
'gene_id' => 'CV00G61210',
'e_value' => '5e-13',
'bit_score' => '65.5',
'alignment_length' => '83',
'identity_percentage' => '38.55',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'TP07G02910' => array(
'gene_id' => 'TP07G02910',
'e_value' => '6e-13',
'bit_score' => '64.7',
'alignment_length' => '108',
'identity_percentage' => '38.89',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P079127'
)
),
'AP00G00630' => array(
'gene_id' => 'AP00G00630',
'e_value' => '1e-12',
'bit_score' => '67.0',
'alignment_length' => '67',
'identity_percentage' => '47.76',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FC009G01340' => array(
'gene_id' => 'FC009G01340',
'e_value' => '2e-11',
'bit_score' => '61.6',
'alignment_length' => '91',
'identity_percentage' => '38.46',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'gsu74830' => array(
'gene_id' => 'gsu74830',
'e_value' => '2e-09',
'bit_score' => '55.8',
'alignment_length' => '88',
'identity_percentage' => '39.77',
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte492450' => array(
'gene_id' => 'pte492450',
'e_value' => '6e-09',
'bit_score' => '55.1',
'alignment_length' => '85',
'identity_percentage' => '35.29',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte317770' => array(
'gene_id' => 'pte317770',
'e_value' => '1e-08',
'bit_score' => '54.3',
'alignment_length' => '92',
'identity_percentage' => '32.61',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'YPL157W' => array(
'gene_id' => 'YPL157W',
'e_value' => '3e-07',
'bit_score' => '50.4',
'alignment_length' => '90',
'identity_percentage' => '36.67',
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
)
)
$similarity_hits_species = array(
'olu' => array(
(int) 0 => 'OL02G04740'
),
'ota' => array(
(int) 0 => 'OT_02G01350'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_14G03340'
),
'ptri' => array(
(int) 0 => 'PTI_22G00250',
(int) 1 => 'PTI_22G00920'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000028233',
(int) 1 => 'ENSMUSG00000093862'
),
'emh' => array(
(int) 0 => 'emh729020'
),
'orcc809' => array(
(int) 0 => 'ORCC809_02G02560'
),
'acg' => array(
(int) 0 => 'AC00G95840'
),
'ath' => array(
(int) 0 => 'AT1G30550',
(int) 1 => 'AT1G45231'
),
'aan' => array(
(int) 0 => 'AA0018G01160'
),
'tps' => array(
(int) 0 => 'TP02G08210',
(int) 1 => 'TP07G02910'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.19g00730'
),
'drm' => array(
(int) 0 => 'FBgn0266195'
),
'atr' => array(
(int) 0 => 'ATR_00003G02210',
(int) 1 => 'ATR_00019G00550'
),
'scp' => array(
(int) 0 => 'SPAC2G11.15c'
),
'pse3' => array(
(int) 0 => 'PI00G01490'
),
'mpu' => array(
(int) 0 => 'MP02G06160'
),
'ppa' => array(
(int) 0 => 'PP00092G00090'
),
'ddi' => array(
(int) 0 => 'DDB_G0288547'
),
'ome' => array(
(int) 0 => 'OM_04G01940'
),
'phs' => array(
(int) 0 => 'phs121750'
),
'esi' => array(
(int) 0 => 'ES0120G00110'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_01G06910'
),
'osa' => array(
(int) 0 => 'OS03G27930',
(int) 1 => 'OS06G08800'
),
'cel' => array(
(int) 0 => 'WBGene00011631'
),
'nga' => array(
(int) 0 => 'Naga_100003g58'
),
'ccr' => array(
(int) 0 => 'ccr132780'
),
'fcy' => array(
(int) 0 => 'FC004G05310',
(int) 1 => 'FC009G01340'
),
'cre' => array(
(int) 0 => 'CR06G11280'
),
'cvu' => array(
(int) 0 => 'CV00G61210'
),
'apr' => array(
(int) 0 => 'AP00G00630'
),
'gsu' => array(
(int) 0 => 'gsu74830'
),
'pte' => array(
(int) 0 => 'pte492450',
(int) 1 => 'pte317770'
),
'sac' => array(
(int) 0 => 'YPL157W'
)
)
$gene_id = 'OL02G04740'
$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 = 'OL02G04740'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'OM_SOC01G00190'
$gf_placeholder = 'HOM03P007387'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-16',
'bit_score' => '77.0',
'alignment_length' => '93',
'identity_percentage' => '44.09',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00080'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146
Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]Code Context echo "<td><input type='checkbox' name='selected_genes[]' value='".$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(
'OL02G04740' => array(
'gene_id' => 'OL02G04740',
'e_value' => '9e-63',
'bit_score' => '191',
'alignment_length' => '91',
'identity_percentage' => '100.00',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'OT_02G01350' => array(
'gene_id' => 'OT_02G01350',
'e_value' => '2e-35',
'bit_score' => '126',
'alignment_length' => '93',
'identity_percentage' => '64.52',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'BPRRCC1105_14G03340' => array(
'gene_id' => 'BPRRCC1105_14G03340',
'e_value' => '3e-22',
'bit_score' => '90.9',
'alignment_length' => '89',
'identity_percentage' => '47.19',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
[maximum depth reached]
)
),
'PTI_22G00250' => array(
'gene_id' => 'PTI_22G00250',
'e_value' => '3e-20',
'bit_score' => '88.6',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000028233' => array(
'gene_id' => 'ENSMUSG00000028233',
'e_value' => '9e-20',
'bit_score' => '88.2',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000093862' => array(
'gene_id' => 'ENSMUSG00000093862',
'e_value' => '1e-19',
'bit_score' => '87.4',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'emh729020' => array(
'gene_id' => 'emh729020',
'e_value' => '2e-19',
'bit_score' => '84.7',
'alignment_length' => '89',
'identity_percentage' => '47.19',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_02G02560' => array(
'gene_id' => 'ORCC809_02G02560',
'e_value' => '9e-19',
'bit_score' => '79.0',
'alignment_length' => '82',
'identity_percentage' => '50.00',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'AC00G95840' => array(
'gene_id' => 'AC00G95840',
'e_value' => '1e-18',
'bit_score' => '80.9',
'alignment_length' => '91',
'identity_percentage' => '45.05',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'AT1G30550' => array(
'gene_id' => 'AT1G30550',
'e_value' => '3e-18',
'bit_score' => '82.8',
'alignment_length' => '91',
'identity_percentage' => '49.45',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AA0018G01160' => array(
'gene_id' => 'AA0018G01160',
'e_value' => '2e-17',
'bit_score' => '75.9',
'alignment_length' => '89',
'identity_percentage' => '46.07',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'TP02G08210' => array(
'gene_id' => 'TP02G08210',
'e_value' => '3e-17',
'bit_score' => '78.2',
'alignment_length' => '93',
'identity_percentage' => '43.01',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.19g00730' => array(
'gene_id' => 'RCC4223.19g00730',
'e_value' => '5e-17',
'bit_score' => '79.3',
'alignment_length' => '84',
'identity_percentage' => '50.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'FBgn0266195' => array(
'gene_id' => 'FBgn0266195',
'e_value' => '9e-17',
'bit_score' => '78.6',
'alignment_length' => '91',
'identity_percentage' => '45.05',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
[maximum depth reached]
)
),
'AT1G45231' => array(
'gene_id' => 'AT1G45231',
'e_value' => '1e-16',
'bit_score' => '78.2',
'alignment_length' => '91',
'identity_percentage' => '43.96',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_044G00080' => array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-16',
'bit_score' => '77.0',
'alignment_length' => '93',
'identity_percentage' => '44.09',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00003G02210' => array(
'gene_id' => 'ATR_00003G02210',
'e_value' => '2e-16',
'bit_score' => '78.2',
'alignment_length' => '90',
'identity_percentage' => '41.11',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'SPAC2G11.15c' => array(
'gene_id' => 'SPAC2G11.15c',
'e_value' => '2e-16',
'bit_score' => '75.5',
'alignment_length' => '91',
'identity_percentage' => '42.86',
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'gf' => array(
[maximum depth reached]
)
),
'PI00G01490' => array(
'gene_id' => 'PI00G01490',
'e_value' => '2e-16',
'bit_score' => '77.8',
'alignment_length' => '88',
'identity_percentage' => '47.73',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'MP02G06160' => array(
'gene_id' => 'MP02G06160',
'e_value' => '3e-16',
'bit_score' => '75.9',
'alignment_length' => '110',
'identity_percentage' => '40.91',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'PP00092G00090' => array(
'gene_id' => 'PP00092G00090',
'e_value' => '3e-16',
'bit_score' => '77.8',
'alignment_length' => '89',
'identity_percentage' => '44.94',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0288547' => array(
'gene_id' => 'DDB_G0288547',
'e_value' => '5e-16',
'bit_score' => '75.1',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'OM_04G01940' => array(
'gene_id' => 'OM_04G01940',
'e_value' => '1e-15',
'bit_score' => '73.9',
'alignment_length' => '95',
'identity_percentage' => '42.11',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'phs121750' => array(
'gene_id' => 'phs121750',
'e_value' => '6e-15',
'bit_score' => '73.2',
'alignment_length' => '90',
'identity_percentage' => '43.33',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00019G00550' => array(
'gene_id' => 'ATR_00019G00550',
'e_value' => '6e-15',
'bit_score' => '72.0',
'alignment_length' => '89',
'identity_percentage' => '42.70',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'ES0120G00110' => array(
'gene_id' => 'ES0120G00110',
'e_value' => '7e-15',
'bit_score' => '73.6',
'alignment_length' => '90',
'identity_percentage' => '44.44',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_01G06910' => array(
'gene_id' => 'MRCC299_01G06910',
'e_value' => '1e-14',
'bit_score' => '72.8',
'alignment_length' => '104',
'identity_percentage' => '41.35',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'OS03G27930' => array(
'gene_id' => 'OS03G27930',
'e_value' => '1e-14',
'bit_score' => '73.2',
'alignment_length' => '89',
'identity_percentage' => '41.57',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'WBGene00011631' => array(
'gene_id' => 'WBGene00011631',
'e_value' => '3e-14',
'bit_score' => '71.6',
'alignment_length' => '90',
'identity_percentage' => '45.56',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100003g58' => array(
'gene_id' => 'Naga_100003g58',
'e_value' => '3e-14',
'bit_score' => '71.2',
'alignment_length' => '89',
'identity_percentage' => '46.07',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'ccr132780' => array(
'gene_id' => 'ccr132780',
'e_value' => '3e-14',
'bit_score' => '69.3',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
[maximum depth reached]
)
),
'FC004G05310' => array(
'gene_id' => 'FC004G05310',
'e_value' => '6e-14',
'bit_score' => '68.6',
'alignment_length' => '91',
'identity_percentage' => '42.86',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'PTI_22G00920' => array(
'gene_id' => 'PTI_22G00920',
'e_value' => '7e-14',
'bit_score' => '69.7',
'alignment_length' => '89',
'identity_percentage' => '44.94',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'OS06G08800' => array(
'gene_id' => 'OS06G08800',
'e_value' => '2e-13',
'bit_score' => '67.8',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'CR06G11280' => array(
'gene_id' => 'CR06G11280',
'e_value' => '5e-13',
'bit_score' => '68.9',
'alignment_length' => '96',
'identity_percentage' => '41.67',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'CV00G61210' => array(
'gene_id' => 'CV00G61210',
'e_value' => '5e-13',
'bit_score' => '65.5',
'alignment_length' => '83',
'identity_percentage' => '38.55',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'TP07G02910' => array(
'gene_id' => 'TP07G02910',
'e_value' => '6e-13',
'bit_score' => '64.7',
'alignment_length' => '108',
'identity_percentage' => '38.89',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'AP00G00630' => array(
'gene_id' => 'AP00G00630',
'e_value' => '1e-12',
'bit_score' => '67.0',
'alignment_length' => '67',
'identity_percentage' => '47.76',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'FC009G01340' => array(
'gene_id' => 'FC009G01340',
'e_value' => '2e-11',
'bit_score' => '61.6',
'alignment_length' => '91',
'identity_percentage' => '38.46',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'gsu74830' => array(
'gene_id' => 'gsu74830',
'e_value' => '2e-09',
'bit_score' => '55.8',
'alignment_length' => '88',
'identity_percentage' => '39.77',
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'gf' => array(
[maximum depth reached]
)
),
'pte492450' => array(
'gene_id' => 'pte492450',
'e_value' => '6e-09',
'bit_score' => '55.1',
'alignment_length' => '85',
'identity_percentage' => '35.29',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'pte317770' => array(
'gene_id' => 'pte317770',
'e_value' => '1e-08',
'bit_score' => '54.3',
'alignment_length' => '92',
'identity_percentage' => '32.61',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
[maximum depth reached]
)
),
'YPL157W' => array(
'gene_id' => 'YPL157W',
'e_value' => '3e-07',
'bit_score' => '50.4',
'alignment_length' => '90',
'identity_percentage' => '36.67',
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'olu' => array(
(int) 0 => 'OL02G04740'
),
'ota' => array(
(int) 0 => 'OT_02G01350'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_14G03340'
),
'ptri' => array(
(int) 0 => 'PTI_22G00250',
(int) 1 => 'PTI_22G00920'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000028233',
(int) 1 => 'ENSMUSG00000093862'
),
'emh' => array(
(int) 0 => 'emh729020'
),
'orcc809' => array(
(int) 0 => 'ORCC809_02G02560'
),
'acg' => array(
(int) 0 => 'AC00G95840'
),
'ath' => array(
(int) 0 => 'AT1G30550',
(int) 1 => 'AT1G45231'
),
'aan' => array(
(int) 0 => 'AA0018G01160'
),
'tps' => array(
(int) 0 => 'TP02G08210',
(int) 1 => 'TP07G02910'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.19g00730'
),
'drm' => array(
(int) 0 => 'FBgn0266195'
),
'atr' => array(
(int) 0 => 'ATR_00003G02210',
(int) 1 => 'ATR_00019G00550'
),
'scp' => array(
(int) 0 => 'SPAC2G11.15c'
),
'pse3' => array(
(int) 0 => 'PI00G01490'
),
'mpu' => array(
(int) 0 => 'MP02G06160'
),
'ppa' => array(
(int) 0 => 'PP00092G00090'
),
'ddi' => array(
(int) 0 => 'DDB_G0288547'
),
'ome' => array(
(int) 0 => 'OM_04G01940'
),
'phs' => array(
(int) 0 => 'phs121750'
),
'esi' => array(
(int) 0 => 'ES0120G00110'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_01G06910'
),
'osa' => array(
(int) 0 => 'OS03G27930',
(int) 1 => 'OS06G08800'
),
'cel' => array(
(int) 0 => 'WBGene00011631'
),
'nga' => array(
(int) 0 => 'Naga_100003g58'
),
'ccr' => array(
(int) 0 => 'ccr132780'
),
'fcy' => array(
(int) 0 => 'FC004G05310',
(int) 1 => 'FC009G01340'
),
'cre' => array(
(int) 0 => 'CR06G11280'
),
'cvu' => array(
(int) 0 => 'CV00G61210'
),
'apr' => array(
(int) 0 => 'AP00G00630'
),
'gsu' => array(
(int) 0 => 'gsu74830'
),
'pte' => array(
(int) 0 => 'pte492450',
(int) 1 => 'pte317770'
),
'sac' => array(
(int) 0 => 'YPL157W'
)
),
'gene_id' => 'OL02G04740',
'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' => 'OL02G04740',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'OM_SOC01G00190',
'gf_placeholder' => 'HOM03P007387',
'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(
'OL02G04740' => array(
'gene_id' => 'OL02G04740',
'e_value' => '9e-63',
'bit_score' => '191',
'alignment_length' => '91',
'identity_percentage' => '100.00',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OT_02G01350' => array(
'gene_id' => 'OT_02G01350',
'e_value' => '2e-35',
'bit_score' => '126',
'alignment_length' => '93',
'identity_percentage' => '64.52',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'BPRRCC1105_14G03340' => array(
'gene_id' => 'BPRRCC1105_14G03340',
'e_value' => '3e-22',
'bit_score' => '90.9',
'alignment_length' => '89',
'identity_percentage' => '47.19',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PTI_22G00250' => array(
'gene_id' => 'PTI_22G00250',
'e_value' => '3e-20',
'bit_score' => '88.6',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P064266'
)
),
'ENSMUSG00000028233' => array(
'gene_id' => 'ENSMUSG00000028233',
'e_value' => '9e-20',
'bit_score' => '88.2',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ENSMUSG00000093862' => array(
'gene_id' => 'ENSMUSG00000093862',
'e_value' => '1e-19',
'bit_score' => '87.4',
'alignment_length' => '91',
'identity_percentage' => '50.55',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'emh729020' => array(
'gene_id' => 'emh729020',
'e_value' => '2e-19',
'bit_score' => '84.7',
'alignment_length' => '89',
'identity_percentage' => '47.19',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ORCC809_02G02560' => array(
'gene_id' => 'ORCC809_02G02560',
'e_value' => '9e-19',
'bit_score' => '79.0',
'alignment_length' => '82',
'identity_percentage' => '50.00',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AC00G95840' => array(
'gene_id' => 'AC00G95840',
'e_value' => '1e-18',
'bit_score' => '80.9',
'alignment_length' => '91',
'identity_percentage' => '45.05',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AT1G30550' => array(
'gene_id' => 'AT1G30550',
'e_value' => '3e-18',
'bit_score' => '82.8',
'alignment_length' => '91',
'identity_percentage' => '49.45',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AA0018G01160' => array(
'gene_id' => 'AA0018G01160',
'e_value' => '2e-17',
'bit_score' => '75.9',
'alignment_length' => '89',
'identity_percentage' => '46.07',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'TP02G08210' => array(
'gene_id' => 'TP02G08210',
'e_value' => '3e-17',
'bit_score' => '78.2',
'alignment_length' => '93',
'identity_percentage' => '43.01',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'RCC4223.19g00730' => array(
'gene_id' => 'RCC4223.19g00730',
'e_value' => '5e-17',
'bit_score' => '79.3',
'alignment_length' => '84',
'identity_percentage' => '50.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FBgn0266195' => array(
'gene_id' => 'FBgn0266195',
'e_value' => '9e-17',
'bit_score' => '78.6',
'alignment_length' => '91',
'identity_percentage' => '45.05',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'AT1G45231' => array(
'gene_id' => 'AT1G45231',
'e_value' => '1e-16',
'bit_score' => '78.2',
'alignment_length' => '91',
'identity_percentage' => '43.96',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CNC64A_044G00080' => array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-16',
'bit_score' => '77.0',
'alignment_length' => '93',
'identity_percentage' => '44.09',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ATR_00003G02210' => array(
'gene_id' => 'ATR_00003G02210',
'e_value' => '2e-16',
'bit_score' => '78.2',
'alignment_length' => '90',
'identity_percentage' => '41.11',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'SPAC2G11.15c' => array(
'gene_id' => 'SPAC2G11.15c',
'e_value' => '2e-16',
'bit_score' => '75.5',
'alignment_length' => '91',
'identity_percentage' => '42.86',
'species' => 'scp',
'common_name' => 'Schizosaccharomyces pombe',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PI00G01490' => array(
'gene_id' => 'PI00G01490',
'e_value' => '2e-16',
'bit_score' => '77.8',
'alignment_length' => '88',
'identity_percentage' => '47.73',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'MP02G06160' => array(
'gene_id' => 'MP02G06160',
'e_value' => '3e-16',
'bit_score' => '75.9',
'alignment_length' => '110',
'identity_percentage' => '40.91',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'PP00092G00090' => array(
'gene_id' => 'PP00092G00090',
'e_value' => '3e-16',
'bit_score' => '77.8',
'alignment_length' => '89',
'identity_percentage' => '44.94',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'DDB_G0288547' => array(
'gene_id' => 'DDB_G0288547',
'e_value' => '5e-16',
'bit_score' => '75.1',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OM_04G01940' => array(
'gene_id' => 'OM_04G01940',
'e_value' => '1e-15',
'bit_score' => '73.9',
'alignment_length' => '95',
'identity_percentage' => '42.11',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'phs121750' => array(
'gene_id' => 'phs121750',
'e_value' => '6e-15',
'bit_score' => '73.2',
'alignment_length' => '90',
'identity_percentage' => '43.33',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ATR_00019G00550' => array(
'gene_id' => 'ATR_00019G00550',
'e_value' => '6e-15',
'bit_score' => '72.0',
'alignment_length' => '89',
'identity_percentage' => '42.70',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ES0120G00110' => array(
'gene_id' => 'ES0120G00110',
'e_value' => '7e-15',
'bit_score' => '73.6',
'alignment_length' => '90',
'identity_percentage' => '44.44',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'MRCC299_01G06910' => array(
'gene_id' => 'MRCC299_01G06910',
'e_value' => '1e-14',
'bit_score' => '72.8',
'alignment_length' => '104',
'identity_percentage' => '41.35',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OS03G27930' => array(
'gene_id' => 'OS03G27930',
'e_value' => '1e-14',
'bit_score' => '73.2',
'alignment_length' => '89',
'identity_percentage' => '41.57',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'WBGene00011631' => array(
'gene_id' => 'WBGene00011631',
'e_value' => '3e-14',
'bit_score' => '71.6',
'alignment_length' => '90',
'identity_percentage' => '45.56',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'Naga_100003g58' => array(
'gene_id' => 'Naga_100003g58',
'e_value' => '3e-14',
'bit_score' => '71.2',
'alignment_length' => '89',
'identity_percentage' => '46.07',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'ccr132780' => array(
'gene_id' => 'ccr132780',
'e_value' => '3e-14',
'bit_score' => '69.3',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'ccr',
'common_name' => 'Chondrus crispus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FC004G05310' => array(
'gene_id' => 'FC004G05310',
'e_value' => '6e-14',
'bit_score' => '68.6',
'alignment_length' => '91',
'identity_percentage' => '42.86',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P064266'
)
),
'PTI_22G00920' => array(
'gene_id' => 'PTI_22G00920',
'e_value' => '7e-14',
'bit_score' => '69.7',
'alignment_length' => '89',
'identity_percentage' => '44.94',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'OS06G08800' => array(
'gene_id' => 'OS06G08800',
'e_value' => '2e-13',
'bit_score' => '67.8',
'alignment_length' => '91',
'identity_percentage' => '41.76',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CR06G11280' => array(
'gene_id' => 'CR06G11280',
'e_value' => '5e-13',
'bit_score' => '68.9',
'alignment_length' => '96',
'identity_percentage' => '41.67',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'CV00G61210' => array(
'gene_id' => 'CV00G61210',
'e_value' => '5e-13',
'bit_score' => '65.5',
'alignment_length' => '83',
'identity_percentage' => '38.55',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'TP07G02910' => array(
'gene_id' => 'TP07G02910',
'e_value' => '6e-13',
'bit_score' => '64.7',
'alignment_length' => '108',
'identity_percentage' => '38.89',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P079127'
)
),
'AP00G00630' => array(
'gene_id' => 'AP00G00630',
'e_value' => '1e-12',
'bit_score' => '67.0',
'alignment_length' => '67',
'identity_percentage' => '47.76',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'FC009G01340' => array(
'gene_id' => 'FC009G01340',
'e_value' => '2e-11',
'bit_score' => '61.6',
'alignment_length' => '91',
'identity_percentage' => '38.46',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'gsu74830' => array(
'gene_id' => 'gsu74830',
'e_value' => '2e-09',
'bit_score' => '55.8',
'alignment_length' => '88',
'identity_percentage' => '39.77',
'species' => 'gsu',
'common_name' => 'Galdieria sulphuraria',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte492450' => array(
'gene_id' => 'pte492450',
'e_value' => '6e-09',
'bit_score' => '55.1',
'alignment_length' => '85',
'identity_percentage' => '35.29',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'pte317770' => array(
'gene_id' => 'pte317770',
'e_value' => '1e-08',
'bit_score' => '54.3',
'alignment_length' => '92',
'identity_percentage' => '32.61',
'species' => 'pte',
'common_name' => 'Paramecium tetraurelia',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
),
'YPL157W' => array(
'gene_id' => 'YPL157W',
'e_value' => '3e-07',
'bit_score' => '50.4',
'alignment_length' => '90',
'identity_percentage' => '36.67',
'species' => 'sac',
'common_name' => 'Saccharomyces cerevisiae strain S288C',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
)
)
$similarity_hits_species = array(
'olu' => array(
(int) 0 => 'OL02G04740'
),
'ota' => array(
(int) 0 => 'OT_02G01350'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_14G03340'
),
'ptri' => array(
(int) 0 => 'PTI_22G00250',
(int) 1 => 'PTI_22G00920'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000028233',
(int) 1 => 'ENSMUSG00000093862'
),
'emh' => array(
(int) 0 => 'emh729020'
),
'orcc809' => array(
(int) 0 => 'ORCC809_02G02560'
),
'acg' => array(
(int) 0 => 'AC00G95840'
),
'ath' => array(
(int) 0 => 'AT1G30550',
(int) 1 => 'AT1G45231'
),
'aan' => array(
(int) 0 => 'AA0018G01160'
),
'tps' => array(
(int) 0 => 'TP02G08210',
(int) 1 => 'TP07G02910'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.19g00730'
),
'drm' => array(
(int) 0 => 'FBgn0266195'
),
'atr' => array(
(int) 0 => 'ATR_00003G02210',
(int) 1 => 'ATR_00019G00550'
),
'scp' => array(
(int) 0 => 'SPAC2G11.15c'
),
'pse3' => array(
(int) 0 => 'PI00G01490'
),
'mpu' => array(
(int) 0 => 'MP02G06160'
),
'ppa' => array(
(int) 0 => 'PP00092G00090'
),
'ddi' => array(
(int) 0 => 'DDB_G0288547'
),
'ome' => array(
(int) 0 => 'OM_04G01940'
),
'phs' => array(
(int) 0 => 'phs121750'
),
'esi' => array(
(int) 0 => 'ES0120G00110'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_01G06910'
),
'osa' => array(
(int) 0 => 'OS03G27930',
(int) 1 => 'OS06G08800'
),
'cel' => array(
(int) 0 => 'WBGene00011631'
),
'nga' => array(
(int) 0 => 'Naga_100003g58'
),
'ccr' => array(
(int) 0 => 'ccr132780'
),
'fcy' => array(
(int) 0 => 'FC004G05310',
(int) 1 => 'FC009G01340'
),
'cre' => array(
(int) 0 => 'CR06G11280'
),
'cvu' => array(
(int) 0 => 'CV00G61210'
),
'apr' => array(
(int) 0 => 'AP00G00630'
),
'gsu' => array(
(int) 0 => 'gsu74830'
),
'pte' => array(
(int) 0 => 'pte492450',
(int) 1 => 'pte317770'
),
'sac' => array(
(int) 0 => 'YPL157W'
)
)
$gene_id = 'OL02G04740'
$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 = 'OL02G04740'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'OM_SOC01G00190'
$gf_placeholder = 'HOM03P007387'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_044G00080',
'e_value' => '1e-16',
'bit_score' => '77.0',
'alignment_length' => '93',
'identity_percentage' => '44.09',
'gf' => array(
'HOMFAM' => 'HOM03P001586',
'ORTHOFAM' => 'ORTHO03P000813'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_044G00080'
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
|
1e-16 |
77.0 |
93 |
44.09 |