|
CNC64A_081G00020 |
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(
'PTI_12G00880' => array(
'gene_id' => 'PTI_12G00880',
'e_value' => '0.0',
'bit_score' => '2104',
'alignment_length' => '1029',
'identity_percentage' => '100.00',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'TP07G01900' => array(
'gene_id' => 'TP07G01900',
'e_value' => '3e-54',
'bit_score' => '194',
'alignment_length' => '249',
'identity_percentage' => '43.37',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'AA0012G00100' => array(
'gene_id' => 'AA0012G00100',
'e_value' => '1e-40',
'bit_score' => '156',
'alignment_length' => '253',
'identity_percentage' => '37.15',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'ES0121G00230' => array(
'gene_id' => 'ES0121G00230',
'e_value' => '4e-38',
'bit_score' => '151',
'alignment_length' => '260',
'identity_percentage' => '36.54',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'PI00G42800' => array(
'gene_id' => 'PI00G42800',
'e_value' => '7e-35',
'bit_score' => '142',
'alignment_length' => '308',
'identity_percentage' => '32.79',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'VC00G18880' => array(
'gene_id' => 'VC00G18880',
'e_value' => '1e-34',
'bit_score' => '139',
'alignment_length' => '276',
'identity_percentage' => '34.42',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.07g03960' => array(
'gene_id' => 'RCC4223.07g03960',
'e_value' => '4e-34',
'bit_score' => '140',
'alignment_length' => '307',
'identity_percentage' => '33.22',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'CV00G91850' => array(
'gene_id' => 'CV00G91850',
'e_value' => '1e-33',
'bit_score' => '136',
'alignment_length' => '268',
'identity_percentage' => '35.82',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'VC00G18900' => array(
'gene_id' => 'VC00G18900',
'e_value' => '2e-33',
'bit_score' => '137',
'alignment_length' => '277',
'identity_percentage' => '34.66',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'ES0121G00040' => array(
'gene_id' => 'ES0121G00040',
'e_value' => '4e-33',
'bit_score' => '138',
'alignment_length' => '269',
'identity_percentage' => '33.46',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_005G01530' => array(
'gene_id' => 'CNC64A_005G01530',
'e_value' => '7e-33',
'bit_score' => '137',
'alignment_length' => '256',
'identity_percentage' => '37.11',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_001G03160' => array(
'gene_id' => 'CNC64A_001G03160',
'e_value' => '1e-32',
'bit_score' => '136',
'alignment_length' => '263',
'identity_percentage' => '35.36',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0280263' => array(
'gene_id' => 'DDB_G0280263',
'e_value' => '1e-31',
'bit_score' => '130',
'alignment_length' => '241',
'identity_percentage' => '35.68',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'PI00G30540' => array(
'gene_id' => 'PI00G30540',
'e_value' => '3e-30',
'bit_score' => '129',
'alignment_length' => '297',
'identity_percentage' => '29.97',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.03g07040' => array(
'gene_id' => 'RCC4223.03g07040',
'e_value' => '6e-30',
'bit_score' => '127',
'alignment_length' => '285',
'identity_percentage' => '30.18',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.03g08350' => array(
'gene_id' => 'RCC4223.03g08350',
'e_value' => '1e-28',
'bit_score' => '123',
'alignment_length' => '325',
'identity_percentage' => '29.85',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G33460' => array(
'gene_id' => 'PI00G33460',
'e_value' => '1e-28',
'bit_score' => '127',
'alignment_length' => '299',
'identity_percentage' => '30.43',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'HE0000G06670' => array(
'gene_id' => 'HE0000G06670',
'e_value' => '2e-28',
'bit_score' => '120',
'alignment_length' => '232',
'identity_percentage' => '35.34',
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'gf' => array(
[maximum depth reached]
)
),
'PI00G29440' => array(
'gene_id' => 'PI00G29440',
'e_value' => '3e-28',
'bit_score' => '122',
'alignment_length' => '298',
'identity_percentage' => '29.87',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'AA0007G00910' => array(
'gene_id' => 'AA0007G00910',
'e_value' => '4e-28',
'bit_score' => '120',
'alignment_length' => '254',
'identity_percentage' => '37.01',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.01g01950' => array(
'gene_id' => 'RCC4223.01g01950',
'e_value' => '2e-27',
'bit_score' => '123',
'alignment_length' => '303',
'identity_percentage' => '30.03',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.07g03950' => array(
'gene_id' => 'RCC4223.07g03950',
'e_value' => '4e-26',
'bit_score' => '116',
'alignment_length' => '356',
'identity_percentage' => '27.53',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G42810' => array(
'gene_id' => 'PI00G42810',
'e_value' => '5e-26',
'bit_score' => '115',
'alignment_length' => '352',
'identity_percentage' => '27.84',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'emh173790' => array(
'gene_id' => 'emh173790',
'e_value' => '7e-26',
'bit_score' => '116',
'alignment_length' => '264',
'identity_percentage' => '34.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.02g06100' => array(
'gene_id' => 'RCC4223.02g06100',
'e_value' => '1e-25',
'bit_score' => '117',
'alignment_length' => '315',
'identity_percentage' => '29.84',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'emh664230' => array(
'gene_id' => 'emh664230',
'e_value' => '2e-25',
'bit_score' => '117',
'alignment_length' => '264',
'identity_percentage' => '34.47',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'emh466680' => array(
'gene_id' => 'emh466680',
'e_value' => '2e-25',
'bit_score' => '118',
'alignment_length' => '254',
'identity_percentage' => '33.07',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'AA0002G06930' => array(
'gene_id' => 'AA0002G06930',
'e_value' => '4e-25',
'bit_score' => '112',
'alignment_length' => '251',
'identity_percentage' => '32.27',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.01g05230' => array(
'gene_id' => 'RCC4223.01g05230',
'e_value' => '8e-25',
'bit_score' => '112',
'alignment_length' => '278',
'identity_percentage' => '34.17',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G47900' => array(
'gene_id' => 'PI00G47900',
'e_value' => '8e-25',
'bit_score' => '112',
'alignment_length' => '278',
'identity_percentage' => '34.53',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'emh62480' => array(
'gene_id' => 'emh62480',
'e_value' => '9e-25',
'bit_score' => '115',
'alignment_length' => '224',
'identity_percentage' => '35.27',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'AA0011G02170' => array(
'gene_id' => 'AA0011G02170',
'e_value' => '2e-24',
'bit_score' => '108',
'alignment_length' => '216',
'identity_percentage' => '31.94',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'emh572420' => array(
'gene_id' => 'emh572420',
'e_value' => '4e-24',
'bit_score' => '113',
'alignment_length' => '224',
'identity_percentage' => '35.27',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'PI00G15880' => array(
'gene_id' => 'PI00G15880',
'e_value' => '1e-23',
'bit_score' => '111',
'alignment_length' => '307',
'identity_percentage' => '29.32',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_081G00020' => array(
'gene_id' => 'CNC64A_081G00020',
'e_value' => '2e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'gf' => array(
[maximum depth reached]
)
),
'AA0017G01560' => array(
'gene_id' => 'AA0017G01560',
'e_value' => '3e-23',
'bit_score' => '105',
'alignment_length' => '255',
'identity_percentage' => '32.55',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'ES0059G00510' => array(
'gene_id' => 'ES0059G00510',
'e_value' => '3e-23',
'bit_score' => '110',
'alignment_length' => '168',
'identity_percentage' => '42.26',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_025G00190' => array(
'gene_id' => 'CNC64A_025G00190',
'e_value' => '7e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_009G00520' => array(
'gene_id' => 'CNC64A_009G00520',
'e_value' => '1e-22',
'bit_score' => '104',
'alignment_length' => '257',
'identity_percentage' => '30.74',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'PTI_20G01150' => array(
'gene_id' => 'PTI_20G01150',
'e_value' => '5e-22',
'bit_score' => '104',
'alignment_length' => '218',
'identity_percentage' => '33.94',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'AP00G23920' => array(
'gene_id' => 'AP00G23920',
'e_value' => '7e-22',
'bit_score' => '102',
'alignment_length' => '284',
'identity_percentage' => '29.23',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'OL16G02020' => array(
'gene_id' => 'OL16G02020',
'e_value' => '2e-21',
'bit_score' => '102',
'alignment_length' => '290',
'identity_percentage' => '30.34',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_16G00660' => array(
'gene_id' => 'ORCC809_16G00660',
'e_value' => '7e-20',
'bit_score' => '98.2',
'alignment_length' => '287',
'identity_percentage' => '29.27',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'OM_17G02230' => array(
'gene_id' => 'OM_17G02230',
'e_value' => '8e-20',
'bit_score' => '99.0',
'alignment_length' => '288',
'identity_percentage' => '29.86',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'PI00G03960' => array(
'gene_id' => 'PI00G03960',
'e_value' => '1e-19',
'bit_score' => '96.3',
'alignment_length' => '326',
'identity_percentage' => '27.61',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'CR02G10720' => array(
'gene_id' => 'CR02G10720',
'e_value' => '2e-18',
'bit_score' => '91.7',
'alignment_length' => '301',
'identity_percentage' => '28.57',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'OT_17G01960' => array(
'gene_id' => 'OT_17G01960',
'e_value' => '3e-14',
'bit_score' => '81.3',
'alignment_length' => '294',
'identity_percentage' => '28.23',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_019G01080' => array(
'gene_id' => 'CNC64A_019G01080',
'e_value' => '8e-14',
'bit_score' => '79.7',
'alignment_length' => '204',
'identity_percentage' => '31.86',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CR03G06520' => array(
'gene_id' => 'CR03G06520',
'e_value' => '1e-11',
'bit_score' => '71.2',
'alignment_length' => '357',
'identity_percentage' => '27.17',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'PI00G65760' => array(
'gene_id' => 'PI00G65760',
'e_value' => '2e-10',
'bit_score' => '67.4',
'alignment_length' => '307',
'identity_percentage' => '23.13',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'PTI_08G03400' => array(
'gene_id' => 'PTI_08G03400',
'e_value' => '3e-10',
'bit_score' => '68.6',
'alignment_length' => '175',
'identity_percentage' => '28.00',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'ES0059G00670' => array(
'gene_id' => 'ES0059G00670',
'e_value' => '3e-10',
'bit_score' => '63.5',
'alignment_length' => '56',
'identity_percentage' => '50.00',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'CR03G07040' => array(
'gene_id' => 'CR03G07040',
'e_value' => '5e-10',
'bit_score' => '67.8',
'alignment_length' => '305',
'identity_percentage' => '27.21',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100043g13' => array(
'gene_id' => 'Naga_100043g13',
'e_value' => '2e-09',
'bit_score' => '65.5',
'alignment_length' => '289',
'identity_percentage' => '25.61',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_05G06940' => array(
'gene_id' => 'MRCC299_05G06940',
'e_value' => '4e-09',
'bit_score' => '64.7',
'alignment_length' => '279',
'identity_percentage' => '27.60',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'ptri' => array(
(int) 0 => 'PTI_12G00880',
(int) 1 => 'PTI_20G01150',
(int) 2 => 'PTI_08G03400'
),
'tps' => array(
(int) 0 => 'TP07G01900'
),
'aan' => array(
(int) 0 => 'AA0012G00100',
(int) 1 => 'AA0007G00910',
(int) 2 => 'AA0002G06930',
(int) 3 => 'AA0011G02170',
(int) 4 => 'AA0017G01560'
),
'esi' => array(
(int) 0 => 'ES0121G00230',
(int) 1 => 'ES0121G00040',
(int) 2 => 'ES0059G00510',
(int) 3 => 'ES0059G00670'
),
'pse3' => array(
(int) 0 => 'PI00G42800',
(int) 1 => 'PI00G30540',
(int) 2 => 'PI00G33460',
(int) 3 => 'PI00G29440',
(int) 4 => 'PI00G42810',
(int) 5 => 'PI00G47900',
(int) 6 => 'PI00G15880',
(int) 7 => 'PI00G03960',
(int) 8 => 'PI00G65760'
),
'vca' => array(
(int) 0 => 'VC00G18880',
(int) 1 => 'VC00G18900'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.07g03960',
(int) 1 => 'RCC4223.03g07040',
(int) 2 => 'RCC4223.03g08350',
(int) 3 => 'RCC4223.01g01950',
(int) 4 => 'RCC4223.07g03950',
(int) 5 => 'RCC4223.02g06100',
(int) 6 => 'RCC4223.01g05230'
),
'cvu' => array(
(int) 0 => 'CV00G91850'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_005G01530',
(int) 1 => 'CNC64A_001G03160',
(int) 2 => 'CNC64A_025G00190',
(int) 3 => 'CNC64A_009G00520',
(int) 4 => 'CNC64A_019G01080'
),
'ddi' => array(
(int) 0 => 'DDB_G0280263'
),
'hsp' => array(
(int) 0 => 'HE0000G06670'
),
'emh' => array(
(int) 0 => 'emh173790',
(int) 1 => 'emh664230',
(int) 2 => 'emh466680',
(int) 3 => 'emh62480',
(int) 4 => 'emh572420'
),
'apr' => array(
(int) 0 => 'AP00G23920'
),
'olu' => array(
(int) 0 => 'OL16G02020'
),
'orcc809' => array(
(int) 0 => 'ORCC809_16G00660'
),
'ome' => array(
(int) 0 => 'OM_17G02230'
),
'cre' => array(
(int) 0 => 'CR02G10720',
(int) 1 => 'CR03G06520',
(int) 2 => 'CR03G07040'
),
'ota' => array(
(int) 0 => 'OT_17G01960'
),
'nga' => array(
(int) 0 => 'Naga_100043g13'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_05G06940'
)
),
'gene_id' => 'PTI_12G00880',
'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' => 'PTI_12G00880',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'CR12G10040',
'gf_placeholder' => 'HOM03P005821',
'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(
'PTI_12G00880' => array(
'gene_id' => 'PTI_12G00880',
'e_value' => '0.0',
'bit_score' => '2104',
'alignment_length' => '1029',
'identity_percentage' => '100.00',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'TP07G01900' => array(
'gene_id' => 'TP07G01900',
'e_value' => '3e-54',
'bit_score' => '194',
'alignment_length' => '249',
'identity_percentage' => '43.37',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'AA0012G00100' => array(
'gene_id' => 'AA0012G00100',
'e_value' => '1e-40',
'bit_score' => '156',
'alignment_length' => '253',
'identity_percentage' => '37.15',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'ES0121G00230' => array(
'gene_id' => 'ES0121G00230',
'e_value' => '4e-38',
'bit_score' => '151',
'alignment_length' => '260',
'identity_percentage' => '36.54',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'PI00G42800' => array(
'gene_id' => 'PI00G42800',
'e_value' => '7e-35',
'bit_score' => '142',
'alignment_length' => '308',
'identity_percentage' => '32.79',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P063421'
)
),
'VC00G18880' => array(
'gene_id' => 'VC00G18880',
'e_value' => '1e-34',
'bit_score' => '139',
'alignment_length' => '276',
'identity_percentage' => '34.42',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'RCC4223.07g03960' => array(
'gene_id' => 'RCC4223.07g03960',
'e_value' => '4e-34',
'bit_score' => '140',
'alignment_length' => '307',
'identity_percentage' => '33.22',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P063421'
)
),
'CV00G91850' => array(
'gene_id' => 'CV00G91850',
'e_value' => '1e-33',
'bit_score' => '136',
'alignment_length' => '268',
'identity_percentage' => '35.82',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'VC00G18900' => array(
'gene_id' => 'VC00G18900',
'e_value' => '2e-33',
'bit_score' => '137',
'alignment_length' => '277',
'identity_percentage' => '34.66',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'ES0121G00040' => array(
'gene_id' => 'ES0121G00040',
'e_value' => '4e-33',
'bit_score' => '138',
'alignment_length' => '269',
'identity_percentage' => '33.46',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'CNC64A_005G01530' => array(
'gene_id' => 'CNC64A_005G01530',
'e_value' => '7e-33',
'bit_score' => '137',
'alignment_length' => '256',
'identity_percentage' => '37.11',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'CNC64A_001G03160' => array(
'gene_id' => 'CNC64A_001G03160',
'e_value' => '1e-32',
'bit_score' => '136',
'alignment_length' => '263',
'identity_percentage' => '35.36',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'DDB_G0280263' => array(
'gene_id' => 'DDB_G0280263',
'e_value' => '1e-31',
'bit_score' => '130',
'alignment_length' => '241',
'identity_percentage' => '35.68',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'PI00G30540' => array(
'gene_id' => 'PI00G30540',
'e_value' => '3e-30',
'bit_score' => '129',
'alignment_length' => '297',
'identity_percentage' => '29.97',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P069753'
)
),
'RCC4223.03g07040' => array(
'gene_id' => 'RCC4223.03g07040',
'e_value' => '6e-30',
'bit_score' => '127',
'alignment_length' => '285',
'identity_percentage' => '30.18',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P069753'
)
),
'RCC4223.03g08350' => array(
'gene_id' => 'RCC4223.03g08350',
'e_value' => '1e-28',
'bit_score' => '123',
'alignment_length' => '325',
'identity_percentage' => '29.85',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P033528'
)
),
'PI00G33460' => array(
'gene_id' => 'PI00G33460',
'e_value' => '1e-28',
'bit_score' => '127',
'alignment_length' => '299',
'identity_percentage' => '30.43',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P073173'
)
),
'HE0000G06670' => array(
'gene_id' => 'HE0000G06670',
'e_value' => '2e-28',
'bit_score' => '120',
'alignment_length' => '232',
'identity_percentage' => '35.34',
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'PI00G29440' => array(
'gene_id' => 'PI00G29440',
'e_value' => '3e-28',
'bit_score' => '122',
'alignment_length' => '298',
'identity_percentage' => '29.87',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P033528'
)
),
'AA0007G00910' => array(
'gene_id' => 'AA0007G00910',
'e_value' => '4e-28',
'bit_score' => '120',
'alignment_length' => '254',
'identity_percentage' => '37.01',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'RCC4223.01g01950' => array(
'gene_id' => 'RCC4223.01g01950',
'e_value' => '2e-27',
'bit_score' => '123',
'alignment_length' => '303',
'identity_percentage' => '30.03',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P073173'
)
),
'RCC4223.07g03950' => array(
'gene_id' => 'RCC4223.07g03950',
'e_value' => '4e-26',
'bit_score' => '116',
'alignment_length' => '356',
'identity_percentage' => '27.53',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P062810'
)
),
'PI00G42810' => array(
'gene_id' => 'PI00G42810',
'e_value' => '5e-26',
'bit_score' => '115',
'alignment_length' => '352',
'identity_percentage' => '27.84',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P062810'
)
),
'emh173790' => array(
'gene_id' => 'emh173790',
'e_value' => '7e-26',
'bit_score' => '116',
'alignment_length' => '264',
'identity_percentage' => '34.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P049315'
)
),
'RCC4223.02g06100' => array(
'gene_id' => 'RCC4223.02g06100',
'e_value' => '1e-25',
'bit_score' => '117',
'alignment_length' => '315',
'identity_percentage' => '29.84',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P069125'
)
),
'emh664230' => array(
'gene_id' => 'emh664230',
'e_value' => '2e-25',
'bit_score' => '117',
'alignment_length' => '264',
'identity_percentage' => '34.47',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P049315'
)
),
'emh466680' => array(
'gene_id' => 'emh466680',
'e_value' => '2e-25',
'bit_score' => '118',
'alignment_length' => '254',
'identity_percentage' => '33.07',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'AA0002G06930' => array(
'gene_id' => 'AA0002G06930',
'e_value' => '4e-25',
'bit_score' => '112',
'alignment_length' => '251',
'identity_percentage' => '32.27',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'RCC4223.01g05230' => array(
'gene_id' => 'RCC4223.01g05230',
'e_value' => '8e-25',
'bit_score' => '112',
'alignment_length' => '278',
'identity_percentage' => '34.17',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'PI00G47900' => array(
'gene_id' => 'PI00G47900',
'e_value' => '8e-25',
'bit_score' => '112',
'alignment_length' => '278',
'identity_percentage' => '34.53',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'emh62480' => array(
'gene_id' => 'emh62480',
'e_value' => '9e-25',
'bit_score' => '115',
'alignment_length' => '224',
'identity_percentage' => '35.27',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'AA0011G02170' => array(
'gene_id' => 'AA0011G02170',
'e_value' => '2e-24',
'bit_score' => '108',
'alignment_length' => '216',
'identity_percentage' => '31.94',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'emh572420' => array(
'gene_id' => 'emh572420',
'e_value' => '4e-24',
'bit_score' => '113',
'alignment_length' => '224',
'identity_percentage' => '35.27',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'PI00G15880' => array(
'gene_id' => 'PI00G15880',
'e_value' => '1e-23',
'bit_score' => '111',
'alignment_length' => '307',
'identity_percentage' => '29.32',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P069125'
)
),
'CNC64A_081G00020' => array(
'gene_id' => 'CNC64A_081G00020',
'e_value' => '2e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P047980'
)
),
'AA0017G01560' => array(
'gene_id' => 'AA0017G01560',
'e_value' => '3e-23',
'bit_score' => '105',
'alignment_length' => '255',
'identity_percentage' => '32.55',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'ES0059G00510' => array(
'gene_id' => 'ES0059G00510',
'e_value' => '3e-23',
'bit_score' => '110',
'alignment_length' => '168',
'identity_percentage' => '42.26',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P071593'
)
),
'CNC64A_025G00190' => array(
'gene_id' => 'CNC64A_025G00190',
'e_value' => '7e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P047980'
)
),
'CNC64A_009G00520' => array(
'gene_id' => 'CNC64A_009G00520',
'e_value' => '1e-22',
'bit_score' => '104',
'alignment_length' => '257',
'identity_percentage' => '30.74',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P071593'
)
),
'PTI_20G01150' => array(
'gene_id' => 'PTI_20G01150',
'e_value' => '5e-22',
'bit_score' => '104',
'alignment_length' => '218',
'identity_percentage' => '33.94',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P143054'
)
),
'AP00G23920' => array(
'gene_id' => 'AP00G23920',
'e_value' => '7e-22',
'bit_score' => '102',
'alignment_length' => '284',
'identity_percentage' => '29.23',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'OL16G02020' => array(
'gene_id' => 'OL16G02020',
'e_value' => '2e-21',
'bit_score' => '102',
'alignment_length' => '290',
'identity_percentage' => '30.34',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'ORCC809_16G00660' => array(
'gene_id' => 'ORCC809_16G00660',
'e_value' => '7e-20',
'bit_score' => '98.2',
'alignment_length' => '287',
'identity_percentage' => '29.27',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'OM_17G02230' => array(
'gene_id' => 'OM_17G02230',
'e_value' => '8e-20',
'bit_score' => '99.0',
'alignment_length' => '288',
'identity_percentage' => '29.86',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'PI00G03960' => array(
'gene_id' => 'PI00G03960',
'e_value' => '1e-19',
'bit_score' => '96.3',
'alignment_length' => '326',
'identity_percentage' => '27.61',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P096624'
)
),
'CR02G10720' => array(
'gene_id' => 'CR02G10720',
'e_value' => '2e-18',
'bit_score' => '91.7',
'alignment_length' => '301',
'identity_percentage' => '28.57',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'OT_17G01960' => array(
'gene_id' => 'OT_17G01960',
'e_value' => '3e-14',
'bit_score' => '81.3',
'alignment_length' => '294',
'identity_percentage' => '28.23',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'CNC64A_019G01080' => array(
'gene_id' => 'CNC64A_019G01080',
'e_value' => '8e-14',
'bit_score' => '79.7',
'alignment_length' => '204',
'identity_percentage' => '31.86',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P012544'
)
),
'CR03G06520' => array(
'gene_id' => 'CR03G06520',
'e_value' => '1e-11',
'bit_score' => '71.2',
'alignment_length' => '357',
'identity_percentage' => '27.17',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P033528'
)
),
'PI00G65760' => array(
'gene_id' => 'PI00G65760',
'e_value' => '2e-10',
'bit_score' => '67.4',
'alignment_length' => '307',
'identity_percentage' => '23.13',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P130752'
)
),
'PTI_08G03400' => array(
'gene_id' => 'PTI_08G03400',
'e_value' => '3e-10',
'bit_score' => '68.6',
'alignment_length' => '175',
'identity_percentage' => '28.00',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P000002',
'ORTHOFAM' => 'ORTHO03P164658'
)
),
'ES0059G00670' => array(
'gene_id' => 'ES0059G00670',
'e_value' => '3e-10',
'bit_score' => '63.5',
'alignment_length' => '56',
'identity_percentage' => '50.00',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P135554'
)
),
'CR03G07040' => array(
'gene_id' => 'CR03G07040',
'e_value' => '5e-10',
'bit_score' => '67.8',
'alignment_length' => '305',
'identity_percentage' => '27.21',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'Naga_100043g13' => array(
'gene_id' => 'Naga_100043g13',
'e_value' => '2e-09',
'bit_score' => '65.5',
'alignment_length' => '289',
'identity_percentage' => '25.61',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P012544'
)
),
'MRCC299_05G06940' => array(
'gene_id' => 'MRCC299_05G06940',
'e_value' => '4e-09',
'bit_score' => '64.7',
'alignment_length' => '279',
'identity_percentage' => '27.60',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
)
)
$similarity_hits_species = array(
'ptri' => array(
(int) 0 => 'PTI_12G00880',
(int) 1 => 'PTI_20G01150',
(int) 2 => 'PTI_08G03400'
),
'tps' => array(
(int) 0 => 'TP07G01900'
),
'aan' => array(
(int) 0 => 'AA0012G00100',
(int) 1 => 'AA0007G00910',
(int) 2 => 'AA0002G06930',
(int) 3 => 'AA0011G02170',
(int) 4 => 'AA0017G01560'
),
'esi' => array(
(int) 0 => 'ES0121G00230',
(int) 1 => 'ES0121G00040',
(int) 2 => 'ES0059G00510',
(int) 3 => 'ES0059G00670'
),
'pse3' => array(
(int) 0 => 'PI00G42800',
(int) 1 => 'PI00G30540',
(int) 2 => 'PI00G33460',
(int) 3 => 'PI00G29440',
(int) 4 => 'PI00G42810',
(int) 5 => 'PI00G47900',
(int) 6 => 'PI00G15880',
(int) 7 => 'PI00G03960',
(int) 8 => 'PI00G65760'
),
'vca' => array(
(int) 0 => 'VC00G18880',
(int) 1 => 'VC00G18900'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.07g03960',
(int) 1 => 'RCC4223.03g07040',
(int) 2 => 'RCC4223.03g08350',
(int) 3 => 'RCC4223.01g01950',
(int) 4 => 'RCC4223.07g03950',
(int) 5 => 'RCC4223.02g06100',
(int) 6 => 'RCC4223.01g05230'
),
'cvu' => array(
(int) 0 => 'CV00G91850'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_005G01530',
(int) 1 => 'CNC64A_001G03160',
(int) 2 => 'CNC64A_025G00190',
(int) 3 => 'CNC64A_009G00520',
(int) 4 => 'CNC64A_019G01080'
),
'ddi' => array(
(int) 0 => 'DDB_G0280263'
),
'hsp' => array(
(int) 0 => 'HE0000G06670'
),
'emh' => array(
(int) 0 => 'emh173790',
(int) 1 => 'emh664230',
(int) 2 => 'emh466680',
(int) 3 => 'emh62480',
(int) 4 => 'emh572420'
),
'apr' => array(
(int) 0 => 'AP00G23920'
),
'olu' => array(
(int) 0 => 'OL16G02020'
),
'orcc809' => array(
(int) 0 => 'ORCC809_16G00660'
),
'ome' => array(
(int) 0 => 'OM_17G02230'
),
'cre' => array(
(int) 0 => 'CR02G10720',
(int) 1 => 'CR03G06520',
(int) 2 => 'CR03G07040'
),
'ota' => array(
(int) 0 => 'OT_17G01960'
),
'nga' => array(
(int) 0 => 'Naga_100043g13'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_05G06940'
)
)
$gene_id = 'PTI_12G00880'
$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 = 'PTI_12G00880'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'CR12G10040'
$gf_placeholder = 'HOM03P005821'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_081G00020',
'e_value' => '2e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P047980'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_081G00020'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146
Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]Code Context echo "<td><input type='checkbox' name='selected_genes[]' value='".$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(
'PTI_12G00880' => array(
'gene_id' => 'PTI_12G00880',
'e_value' => '0.0',
'bit_score' => '2104',
'alignment_length' => '1029',
'identity_percentage' => '100.00',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'TP07G01900' => array(
'gene_id' => 'TP07G01900',
'e_value' => '3e-54',
'bit_score' => '194',
'alignment_length' => '249',
'identity_percentage' => '43.37',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
[maximum depth reached]
)
),
'AA0012G00100' => array(
'gene_id' => 'AA0012G00100',
'e_value' => '1e-40',
'bit_score' => '156',
'alignment_length' => '253',
'identity_percentage' => '37.15',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'ES0121G00230' => array(
'gene_id' => 'ES0121G00230',
'e_value' => '4e-38',
'bit_score' => '151',
'alignment_length' => '260',
'identity_percentage' => '36.54',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'PI00G42800' => array(
'gene_id' => 'PI00G42800',
'e_value' => '7e-35',
'bit_score' => '142',
'alignment_length' => '308',
'identity_percentage' => '32.79',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'VC00G18880' => array(
'gene_id' => 'VC00G18880',
'e_value' => '1e-34',
'bit_score' => '139',
'alignment_length' => '276',
'identity_percentage' => '34.42',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.07g03960' => array(
'gene_id' => 'RCC4223.07g03960',
'e_value' => '4e-34',
'bit_score' => '140',
'alignment_length' => '307',
'identity_percentage' => '33.22',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'CV00G91850' => array(
'gene_id' => 'CV00G91850',
'e_value' => '1e-33',
'bit_score' => '136',
'alignment_length' => '268',
'identity_percentage' => '35.82',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'VC00G18900' => array(
'gene_id' => 'VC00G18900',
'e_value' => '2e-33',
'bit_score' => '137',
'alignment_length' => '277',
'identity_percentage' => '34.66',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'ES0121G00040' => array(
'gene_id' => 'ES0121G00040',
'e_value' => '4e-33',
'bit_score' => '138',
'alignment_length' => '269',
'identity_percentage' => '33.46',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_005G01530' => array(
'gene_id' => 'CNC64A_005G01530',
'e_value' => '7e-33',
'bit_score' => '137',
'alignment_length' => '256',
'identity_percentage' => '37.11',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_001G03160' => array(
'gene_id' => 'CNC64A_001G03160',
'e_value' => '1e-32',
'bit_score' => '136',
'alignment_length' => '263',
'identity_percentage' => '35.36',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0280263' => array(
'gene_id' => 'DDB_G0280263',
'e_value' => '1e-31',
'bit_score' => '130',
'alignment_length' => '241',
'identity_percentage' => '35.68',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'PI00G30540' => array(
'gene_id' => 'PI00G30540',
'e_value' => '3e-30',
'bit_score' => '129',
'alignment_length' => '297',
'identity_percentage' => '29.97',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.03g07040' => array(
'gene_id' => 'RCC4223.03g07040',
'e_value' => '6e-30',
'bit_score' => '127',
'alignment_length' => '285',
'identity_percentage' => '30.18',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.03g08350' => array(
'gene_id' => 'RCC4223.03g08350',
'e_value' => '1e-28',
'bit_score' => '123',
'alignment_length' => '325',
'identity_percentage' => '29.85',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G33460' => array(
'gene_id' => 'PI00G33460',
'e_value' => '1e-28',
'bit_score' => '127',
'alignment_length' => '299',
'identity_percentage' => '30.43',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'HE0000G06670' => array(
'gene_id' => 'HE0000G06670',
'e_value' => '2e-28',
'bit_score' => '120',
'alignment_length' => '232',
'identity_percentage' => '35.34',
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'gf' => array(
[maximum depth reached]
)
),
'PI00G29440' => array(
'gene_id' => 'PI00G29440',
'e_value' => '3e-28',
'bit_score' => '122',
'alignment_length' => '298',
'identity_percentage' => '29.87',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'AA0007G00910' => array(
'gene_id' => 'AA0007G00910',
'e_value' => '4e-28',
'bit_score' => '120',
'alignment_length' => '254',
'identity_percentage' => '37.01',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.01g01950' => array(
'gene_id' => 'RCC4223.01g01950',
'e_value' => '2e-27',
'bit_score' => '123',
'alignment_length' => '303',
'identity_percentage' => '30.03',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.07g03950' => array(
'gene_id' => 'RCC4223.07g03950',
'e_value' => '4e-26',
'bit_score' => '116',
'alignment_length' => '356',
'identity_percentage' => '27.53',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G42810' => array(
'gene_id' => 'PI00G42810',
'e_value' => '5e-26',
'bit_score' => '115',
'alignment_length' => '352',
'identity_percentage' => '27.84',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'emh173790' => array(
'gene_id' => 'emh173790',
'e_value' => '7e-26',
'bit_score' => '116',
'alignment_length' => '264',
'identity_percentage' => '34.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.02g06100' => array(
'gene_id' => 'RCC4223.02g06100',
'e_value' => '1e-25',
'bit_score' => '117',
'alignment_length' => '315',
'identity_percentage' => '29.84',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'emh664230' => array(
'gene_id' => 'emh664230',
'e_value' => '2e-25',
'bit_score' => '117',
'alignment_length' => '264',
'identity_percentage' => '34.47',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'emh466680' => array(
'gene_id' => 'emh466680',
'e_value' => '2e-25',
'bit_score' => '118',
'alignment_length' => '254',
'identity_percentage' => '33.07',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'AA0002G06930' => array(
'gene_id' => 'AA0002G06930',
'e_value' => '4e-25',
'bit_score' => '112',
'alignment_length' => '251',
'identity_percentage' => '32.27',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.01g05230' => array(
'gene_id' => 'RCC4223.01g05230',
'e_value' => '8e-25',
'bit_score' => '112',
'alignment_length' => '278',
'identity_percentage' => '34.17',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G47900' => array(
'gene_id' => 'PI00G47900',
'e_value' => '8e-25',
'bit_score' => '112',
'alignment_length' => '278',
'identity_percentage' => '34.53',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'emh62480' => array(
'gene_id' => 'emh62480',
'e_value' => '9e-25',
'bit_score' => '115',
'alignment_length' => '224',
'identity_percentage' => '35.27',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'AA0011G02170' => array(
'gene_id' => 'AA0011G02170',
'e_value' => '2e-24',
'bit_score' => '108',
'alignment_length' => '216',
'identity_percentage' => '31.94',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'emh572420' => array(
'gene_id' => 'emh572420',
'e_value' => '4e-24',
'bit_score' => '113',
'alignment_length' => '224',
'identity_percentage' => '35.27',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'PI00G15880' => array(
'gene_id' => 'PI00G15880',
'e_value' => '1e-23',
'bit_score' => '111',
'alignment_length' => '307',
'identity_percentage' => '29.32',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_081G00020' => array(
'gene_id' => 'CNC64A_081G00020',
'e_value' => '2e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'gf' => array(
[maximum depth reached]
)
),
'AA0017G01560' => array(
'gene_id' => 'AA0017G01560',
'e_value' => '3e-23',
'bit_score' => '105',
'alignment_length' => '255',
'identity_percentage' => '32.55',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
),
'ES0059G00510' => array(
'gene_id' => 'ES0059G00510',
'e_value' => '3e-23',
'bit_score' => '110',
'alignment_length' => '168',
'identity_percentage' => '42.26',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_025G00190' => array(
'gene_id' => 'CNC64A_025G00190',
'e_value' => '7e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_009G00520' => array(
'gene_id' => 'CNC64A_009G00520',
'e_value' => '1e-22',
'bit_score' => '104',
'alignment_length' => '257',
'identity_percentage' => '30.74',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'PTI_20G01150' => array(
'gene_id' => 'PTI_20G01150',
'e_value' => '5e-22',
'bit_score' => '104',
'alignment_length' => '218',
'identity_percentage' => '33.94',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'AP00G23920' => array(
'gene_id' => 'AP00G23920',
'e_value' => '7e-22',
'bit_score' => '102',
'alignment_length' => '284',
'identity_percentage' => '29.23',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'OL16G02020' => array(
'gene_id' => 'OL16G02020',
'e_value' => '2e-21',
'bit_score' => '102',
'alignment_length' => '290',
'identity_percentage' => '30.34',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_16G00660' => array(
'gene_id' => 'ORCC809_16G00660',
'e_value' => '7e-20',
'bit_score' => '98.2',
'alignment_length' => '287',
'identity_percentage' => '29.27',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'OM_17G02230' => array(
'gene_id' => 'OM_17G02230',
'e_value' => '8e-20',
'bit_score' => '99.0',
'alignment_length' => '288',
'identity_percentage' => '29.86',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'PI00G03960' => array(
'gene_id' => 'PI00G03960',
'e_value' => '1e-19',
'bit_score' => '96.3',
'alignment_length' => '326',
'identity_percentage' => '27.61',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'CR02G10720' => array(
'gene_id' => 'CR02G10720',
'e_value' => '2e-18',
'bit_score' => '91.7',
'alignment_length' => '301',
'identity_percentage' => '28.57',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'OT_17G01960' => array(
'gene_id' => 'OT_17G01960',
'e_value' => '3e-14',
'bit_score' => '81.3',
'alignment_length' => '294',
'identity_percentage' => '28.23',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_019G01080' => array(
'gene_id' => 'CNC64A_019G01080',
'e_value' => '8e-14',
'bit_score' => '79.7',
'alignment_length' => '204',
'identity_percentage' => '31.86',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CR03G06520' => array(
'gene_id' => 'CR03G06520',
'e_value' => '1e-11',
'bit_score' => '71.2',
'alignment_length' => '357',
'identity_percentage' => '27.17',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'PI00G65760' => array(
'gene_id' => 'PI00G65760',
'e_value' => '2e-10',
'bit_score' => '67.4',
'alignment_length' => '307',
'identity_percentage' => '23.13',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'PTI_08G03400' => array(
'gene_id' => 'PTI_08G03400',
'e_value' => '3e-10',
'bit_score' => '68.6',
'alignment_length' => '175',
'identity_percentage' => '28.00',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'ES0059G00670' => array(
'gene_id' => 'ES0059G00670',
'e_value' => '3e-10',
'bit_score' => '63.5',
'alignment_length' => '56',
'identity_percentage' => '50.00',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
[maximum depth reached]
)
),
'CR03G07040' => array(
'gene_id' => 'CR03G07040',
'e_value' => '5e-10',
'bit_score' => '67.8',
'alignment_length' => '305',
'identity_percentage' => '27.21',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100043g13' => array(
'gene_id' => 'Naga_100043g13',
'e_value' => '2e-09',
'bit_score' => '65.5',
'alignment_length' => '289',
'identity_percentage' => '25.61',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_05G06940' => array(
'gene_id' => 'MRCC299_05G06940',
'e_value' => '4e-09',
'bit_score' => '64.7',
'alignment_length' => '279',
'identity_percentage' => '27.60',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'ptri' => array(
(int) 0 => 'PTI_12G00880',
(int) 1 => 'PTI_20G01150',
(int) 2 => 'PTI_08G03400'
),
'tps' => array(
(int) 0 => 'TP07G01900'
),
'aan' => array(
(int) 0 => 'AA0012G00100',
(int) 1 => 'AA0007G00910',
(int) 2 => 'AA0002G06930',
(int) 3 => 'AA0011G02170',
(int) 4 => 'AA0017G01560'
),
'esi' => array(
(int) 0 => 'ES0121G00230',
(int) 1 => 'ES0121G00040',
(int) 2 => 'ES0059G00510',
(int) 3 => 'ES0059G00670'
),
'pse3' => array(
(int) 0 => 'PI00G42800',
(int) 1 => 'PI00G30540',
(int) 2 => 'PI00G33460',
(int) 3 => 'PI00G29440',
(int) 4 => 'PI00G42810',
(int) 5 => 'PI00G47900',
(int) 6 => 'PI00G15880',
(int) 7 => 'PI00G03960',
(int) 8 => 'PI00G65760'
),
'vca' => array(
(int) 0 => 'VC00G18880',
(int) 1 => 'VC00G18900'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.07g03960',
(int) 1 => 'RCC4223.03g07040',
(int) 2 => 'RCC4223.03g08350',
(int) 3 => 'RCC4223.01g01950',
(int) 4 => 'RCC4223.07g03950',
(int) 5 => 'RCC4223.02g06100',
(int) 6 => 'RCC4223.01g05230'
),
'cvu' => array(
(int) 0 => 'CV00G91850'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_005G01530',
(int) 1 => 'CNC64A_001G03160',
(int) 2 => 'CNC64A_025G00190',
(int) 3 => 'CNC64A_009G00520',
(int) 4 => 'CNC64A_019G01080'
),
'ddi' => array(
(int) 0 => 'DDB_G0280263'
),
'hsp' => array(
(int) 0 => 'HE0000G06670'
),
'emh' => array(
(int) 0 => 'emh173790',
(int) 1 => 'emh664230',
(int) 2 => 'emh466680',
(int) 3 => 'emh62480',
(int) 4 => 'emh572420'
),
'apr' => array(
(int) 0 => 'AP00G23920'
),
'olu' => array(
(int) 0 => 'OL16G02020'
),
'orcc809' => array(
(int) 0 => 'ORCC809_16G00660'
),
'ome' => array(
(int) 0 => 'OM_17G02230'
),
'cre' => array(
(int) 0 => 'CR02G10720',
(int) 1 => 'CR03G06520',
(int) 2 => 'CR03G07040'
),
'ota' => array(
(int) 0 => 'OT_17G01960'
),
'nga' => array(
(int) 0 => 'Naga_100043g13'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_05G06940'
)
),
'gene_id' => 'PTI_12G00880',
'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' => 'PTI_12G00880',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'CR12G10040',
'gf_placeholder' => 'HOM03P005821',
'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(
'PTI_12G00880' => array(
'gene_id' => 'PTI_12G00880',
'e_value' => '0.0',
'bit_score' => '2104',
'alignment_length' => '1029',
'identity_percentage' => '100.00',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'TP07G01900' => array(
'gene_id' => 'TP07G01900',
'e_value' => '3e-54',
'bit_score' => '194',
'alignment_length' => '249',
'identity_percentage' => '43.37',
'species' => 'tps',
'common_name' => 'Thalassiosira pseudonana',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'AA0012G00100' => array(
'gene_id' => 'AA0012G00100',
'e_value' => '1e-40',
'bit_score' => '156',
'alignment_length' => '253',
'identity_percentage' => '37.15',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'ES0121G00230' => array(
'gene_id' => 'ES0121G00230',
'e_value' => '4e-38',
'bit_score' => '151',
'alignment_length' => '260',
'identity_percentage' => '36.54',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'PI00G42800' => array(
'gene_id' => 'PI00G42800',
'e_value' => '7e-35',
'bit_score' => '142',
'alignment_length' => '308',
'identity_percentage' => '32.79',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P063421'
)
),
'VC00G18880' => array(
'gene_id' => 'VC00G18880',
'e_value' => '1e-34',
'bit_score' => '139',
'alignment_length' => '276',
'identity_percentage' => '34.42',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'RCC4223.07g03960' => array(
'gene_id' => 'RCC4223.07g03960',
'e_value' => '4e-34',
'bit_score' => '140',
'alignment_length' => '307',
'identity_percentage' => '33.22',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P063421'
)
),
'CV00G91850' => array(
'gene_id' => 'CV00G91850',
'e_value' => '1e-33',
'bit_score' => '136',
'alignment_length' => '268',
'identity_percentage' => '35.82',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'VC00G18900' => array(
'gene_id' => 'VC00G18900',
'e_value' => '2e-33',
'bit_score' => '137',
'alignment_length' => '277',
'identity_percentage' => '34.66',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'ES0121G00040' => array(
'gene_id' => 'ES0121G00040',
'e_value' => '4e-33',
'bit_score' => '138',
'alignment_length' => '269',
'identity_percentage' => '33.46',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'CNC64A_005G01530' => array(
'gene_id' => 'CNC64A_005G01530',
'e_value' => '7e-33',
'bit_score' => '137',
'alignment_length' => '256',
'identity_percentage' => '37.11',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'CNC64A_001G03160' => array(
'gene_id' => 'CNC64A_001G03160',
'e_value' => '1e-32',
'bit_score' => '136',
'alignment_length' => '263',
'identity_percentage' => '35.36',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'DDB_G0280263' => array(
'gene_id' => 'DDB_G0280263',
'e_value' => '1e-31',
'bit_score' => '130',
'alignment_length' => '241',
'identity_percentage' => '35.68',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'PI00G30540' => array(
'gene_id' => 'PI00G30540',
'e_value' => '3e-30',
'bit_score' => '129',
'alignment_length' => '297',
'identity_percentage' => '29.97',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P069753'
)
),
'RCC4223.03g07040' => array(
'gene_id' => 'RCC4223.03g07040',
'e_value' => '6e-30',
'bit_score' => '127',
'alignment_length' => '285',
'identity_percentage' => '30.18',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P069753'
)
),
'RCC4223.03g08350' => array(
'gene_id' => 'RCC4223.03g08350',
'e_value' => '1e-28',
'bit_score' => '123',
'alignment_length' => '325',
'identity_percentage' => '29.85',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P033528'
)
),
'PI00G33460' => array(
'gene_id' => 'PI00G33460',
'e_value' => '1e-28',
'bit_score' => '127',
'alignment_length' => '299',
'identity_percentage' => '30.43',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P073173'
)
),
'HE0000G06670' => array(
'gene_id' => 'HE0000G06670',
'e_value' => '2e-28',
'bit_score' => '120',
'alignment_length' => '232',
'identity_percentage' => '35.34',
'species' => 'hsp',
'common_name' => 'Helicosporidium sp. ',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'PI00G29440' => array(
'gene_id' => 'PI00G29440',
'e_value' => '3e-28',
'bit_score' => '122',
'alignment_length' => '298',
'identity_percentage' => '29.87',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P033528'
)
),
'AA0007G00910' => array(
'gene_id' => 'AA0007G00910',
'e_value' => '4e-28',
'bit_score' => '120',
'alignment_length' => '254',
'identity_percentage' => '37.01',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'RCC4223.01g01950' => array(
'gene_id' => 'RCC4223.01g01950',
'e_value' => '2e-27',
'bit_score' => '123',
'alignment_length' => '303',
'identity_percentage' => '30.03',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P073173'
)
),
'RCC4223.07g03950' => array(
'gene_id' => 'RCC4223.07g03950',
'e_value' => '4e-26',
'bit_score' => '116',
'alignment_length' => '356',
'identity_percentage' => '27.53',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P062810'
)
),
'PI00G42810' => array(
'gene_id' => 'PI00G42810',
'e_value' => '5e-26',
'bit_score' => '115',
'alignment_length' => '352',
'identity_percentage' => '27.84',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P062810'
)
),
'emh173790' => array(
'gene_id' => 'emh173790',
'e_value' => '7e-26',
'bit_score' => '116',
'alignment_length' => '264',
'identity_percentage' => '34.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P049315'
)
),
'RCC4223.02g06100' => array(
'gene_id' => 'RCC4223.02g06100',
'e_value' => '1e-25',
'bit_score' => '117',
'alignment_length' => '315',
'identity_percentage' => '29.84',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P069125'
)
),
'emh664230' => array(
'gene_id' => 'emh664230',
'e_value' => '2e-25',
'bit_score' => '117',
'alignment_length' => '264',
'identity_percentage' => '34.47',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P049315'
)
),
'emh466680' => array(
'gene_id' => 'emh466680',
'e_value' => '2e-25',
'bit_score' => '118',
'alignment_length' => '254',
'identity_percentage' => '33.07',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'AA0002G06930' => array(
'gene_id' => 'AA0002G06930',
'e_value' => '4e-25',
'bit_score' => '112',
'alignment_length' => '251',
'identity_percentage' => '32.27',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'RCC4223.01g05230' => array(
'gene_id' => 'RCC4223.01g05230',
'e_value' => '8e-25',
'bit_score' => '112',
'alignment_length' => '278',
'identity_percentage' => '34.17',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'PI00G47900' => array(
'gene_id' => 'PI00G47900',
'e_value' => '8e-25',
'bit_score' => '112',
'alignment_length' => '278',
'identity_percentage' => '34.53',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'emh62480' => array(
'gene_id' => 'emh62480',
'e_value' => '9e-25',
'bit_score' => '115',
'alignment_length' => '224',
'identity_percentage' => '35.27',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'AA0011G02170' => array(
'gene_id' => 'AA0011G02170',
'e_value' => '2e-24',
'bit_score' => '108',
'alignment_length' => '216',
'identity_percentage' => '31.94',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'emh572420' => array(
'gene_id' => 'emh572420',
'e_value' => '4e-24',
'bit_score' => '113',
'alignment_length' => '224',
'identity_percentage' => '35.27',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'PI00G15880' => array(
'gene_id' => 'PI00G15880',
'e_value' => '1e-23',
'bit_score' => '111',
'alignment_length' => '307',
'identity_percentage' => '29.32',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P069125'
)
),
'CNC64A_081G00020' => array(
'gene_id' => 'CNC64A_081G00020',
'e_value' => '2e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P047980'
)
),
'AA0017G01560' => array(
'gene_id' => 'AA0017G01560',
'e_value' => '3e-23',
'bit_score' => '105',
'alignment_length' => '255',
'identity_percentage' => '32.55',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006259'
)
),
'ES0059G00510' => array(
'gene_id' => 'ES0059G00510',
'e_value' => '3e-23',
'bit_score' => '110',
'alignment_length' => '168',
'identity_percentage' => '42.26',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P071593'
)
),
'CNC64A_025G00190' => array(
'gene_id' => 'CNC64A_025G00190',
'e_value' => '7e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P047980'
)
),
'CNC64A_009G00520' => array(
'gene_id' => 'CNC64A_009G00520',
'e_value' => '1e-22',
'bit_score' => '104',
'alignment_length' => '257',
'identity_percentage' => '30.74',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P071593'
)
),
'PTI_20G01150' => array(
'gene_id' => 'PTI_20G01150',
'e_value' => '5e-22',
'bit_score' => '104',
'alignment_length' => '218',
'identity_percentage' => '33.94',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P006964',
'ORTHOFAM' => 'ORTHO03P143054'
)
),
'AP00G23920' => array(
'gene_id' => 'AP00G23920',
'e_value' => '7e-22',
'bit_score' => '102',
'alignment_length' => '284',
'identity_percentage' => '29.23',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'OL16G02020' => array(
'gene_id' => 'OL16G02020',
'e_value' => '2e-21',
'bit_score' => '102',
'alignment_length' => '290',
'identity_percentage' => '30.34',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'ORCC809_16G00660' => array(
'gene_id' => 'ORCC809_16G00660',
'e_value' => '7e-20',
'bit_score' => '98.2',
'alignment_length' => '287',
'identity_percentage' => '29.27',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'OM_17G02230' => array(
'gene_id' => 'OM_17G02230',
'e_value' => '8e-20',
'bit_score' => '99.0',
'alignment_length' => '288',
'identity_percentage' => '29.86',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'PI00G03960' => array(
'gene_id' => 'PI00G03960',
'e_value' => '1e-19',
'bit_score' => '96.3',
'alignment_length' => '326',
'identity_percentage' => '27.61',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P096624'
)
),
'CR02G10720' => array(
'gene_id' => 'CR02G10720',
'e_value' => '2e-18',
'bit_score' => '91.7',
'alignment_length' => '301',
'identity_percentage' => '28.57',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'OT_17G01960' => array(
'gene_id' => 'OT_17G01960',
'e_value' => '3e-14',
'bit_score' => '81.3',
'alignment_length' => '294',
'identity_percentage' => '28.23',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
),
'CNC64A_019G01080' => array(
'gene_id' => 'CNC64A_019G01080',
'e_value' => '8e-14',
'bit_score' => '79.7',
'alignment_length' => '204',
'identity_percentage' => '31.86',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P012544'
)
),
'CR03G06520' => array(
'gene_id' => 'CR03G06520',
'e_value' => '1e-11',
'bit_score' => '71.2',
'alignment_length' => '357',
'identity_percentage' => '27.17',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P033528'
)
),
'PI00G65760' => array(
'gene_id' => 'PI00G65760',
'e_value' => '2e-10',
'bit_score' => '67.4',
'alignment_length' => '307',
'identity_percentage' => '23.13',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P130752'
)
),
'PTI_08G03400' => array(
'gene_id' => 'PTI_08G03400',
'e_value' => '3e-10',
'bit_score' => '68.6',
'alignment_length' => '175',
'identity_percentage' => '28.00',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P000002',
'ORTHOFAM' => 'ORTHO03P164658'
)
),
'ES0059G00670' => array(
'gene_id' => 'ES0059G00670',
'e_value' => '3e-10',
'bit_score' => '63.5',
'alignment_length' => '56',
'identity_percentage' => '50.00',
'species' => 'esi',
'common_name' => 'Ectocarpus siliculosus',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P135554'
)
),
'CR03G07040' => array(
'gene_id' => 'CR03G07040',
'e_value' => '5e-10',
'bit_score' => '67.8',
'alignment_length' => '305',
'identity_percentage' => '27.21',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P006431'
)
),
'Naga_100043g13' => array(
'gene_id' => 'Naga_100043g13',
'e_value' => '2e-09',
'bit_score' => '65.5',
'alignment_length' => '289',
'identity_percentage' => '25.61',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P012544'
)
),
'MRCC299_05G06940' => array(
'gene_id' => 'MRCC299_05G06940',
'e_value' => '4e-09',
'bit_score' => '64.7',
'alignment_length' => '279',
'identity_percentage' => '27.60',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P012932',
'ORTHOFAM' => 'ORTHO03P012832'
)
)
)
$similarity_hits_species = array(
'ptri' => array(
(int) 0 => 'PTI_12G00880',
(int) 1 => 'PTI_20G01150',
(int) 2 => 'PTI_08G03400'
),
'tps' => array(
(int) 0 => 'TP07G01900'
),
'aan' => array(
(int) 0 => 'AA0012G00100',
(int) 1 => 'AA0007G00910',
(int) 2 => 'AA0002G06930',
(int) 3 => 'AA0011G02170',
(int) 4 => 'AA0017G01560'
),
'esi' => array(
(int) 0 => 'ES0121G00230',
(int) 1 => 'ES0121G00040',
(int) 2 => 'ES0059G00510',
(int) 3 => 'ES0059G00670'
),
'pse3' => array(
(int) 0 => 'PI00G42800',
(int) 1 => 'PI00G30540',
(int) 2 => 'PI00G33460',
(int) 3 => 'PI00G29440',
(int) 4 => 'PI00G42810',
(int) 5 => 'PI00G47900',
(int) 6 => 'PI00G15880',
(int) 7 => 'PI00G03960',
(int) 8 => 'PI00G65760'
),
'vca' => array(
(int) 0 => 'VC00G18880',
(int) 1 => 'VC00G18900'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.07g03960',
(int) 1 => 'RCC4223.03g07040',
(int) 2 => 'RCC4223.03g08350',
(int) 3 => 'RCC4223.01g01950',
(int) 4 => 'RCC4223.07g03950',
(int) 5 => 'RCC4223.02g06100',
(int) 6 => 'RCC4223.01g05230'
),
'cvu' => array(
(int) 0 => 'CV00G91850'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_005G01530',
(int) 1 => 'CNC64A_001G03160',
(int) 2 => 'CNC64A_025G00190',
(int) 3 => 'CNC64A_009G00520',
(int) 4 => 'CNC64A_019G01080'
),
'ddi' => array(
(int) 0 => 'DDB_G0280263'
),
'hsp' => array(
(int) 0 => 'HE0000G06670'
),
'emh' => array(
(int) 0 => 'emh173790',
(int) 1 => 'emh664230',
(int) 2 => 'emh466680',
(int) 3 => 'emh62480',
(int) 4 => 'emh572420'
),
'apr' => array(
(int) 0 => 'AP00G23920'
),
'olu' => array(
(int) 0 => 'OL16G02020'
),
'orcc809' => array(
(int) 0 => 'ORCC809_16G00660'
),
'ome' => array(
(int) 0 => 'OM_17G02230'
),
'cre' => array(
(int) 0 => 'CR02G10720',
(int) 1 => 'CR03G06520',
(int) 2 => 'CR03G07040'
),
'ota' => array(
(int) 0 => 'OT_17G01960'
),
'nga' => array(
(int) 0 => 'Naga_100043g13'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_05G06940'
)
)
$gene_id = 'PTI_12G00880'
$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 = 'PTI_12G00880'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'CR12G10040'
$gf_placeholder = 'HOM03P005821'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_081G00020',
'e_value' => '2e-23',
'bit_score' => '105',
'alignment_length' => '218',
'identity_percentage' => '34.40',
'gf' => array(
'HOMFAM' => 'HOM03P001374',
'ORTHOFAM' => 'ORTHO03P047980'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_081G00020'
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
|
2e-23 |
105 |
218 |
34.40 |