|
CNC64A_094G00020 |
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(
'RCC4223.05g02320' => array(
'gene_id' => 'RCC4223.05g02320',
'e_value' => '0.0',
'bit_score' => '2335',
'alignment_length' => '1128',
'identity_percentage' => '100.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G14610' => array(
'gene_id' => 'PI00G14610',
'e_value' => '0.0',
'bit_score' => '1986',
'alignment_length' => '1128',
'identity_percentage' => '84.93',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'CV00G05540' => array(
'gene_id' => 'CV00G05540',
'e_value' => '4e-86',
'bit_score' => '309',
'alignment_length' => '1018',
'identity_percentage' => '26.72',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_003G00300' => array(
'gene_id' => 'CNC64A_003G00300',
'e_value' => '5e-70',
'bit_score' => '256',
'alignment_length' => '805',
'identity_percentage' => '27.58',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_003G00260' => array(
'gene_id' => 'CNC64A_003G00260',
'e_value' => '2e-69',
'bit_score' => '252',
'alignment_length' => '603',
'identity_percentage' => '30.18',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'AC00G45200' => array(
'gene_id' => 'AC00G45200',
'e_value' => '8e-69',
'bit_score' => '253',
'alignment_length' => '954',
'identity_percentage' => '25.26',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'PP00270G00460' => array(
'gene_id' => 'PP00270G00460',
'e_value' => '3e-53',
'bit_score' => '208',
'alignment_length' => '933',
'identity_percentage' => '24.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00030G00120' => array(
'gene_id' => 'ATR_00030G00120',
'e_value' => '4e-51',
'bit_score' => '201',
'alignment_length' => '842',
'identity_percentage' => '24.35',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'AT5G16280' => array(
'gene_id' => 'AT5G16280',
'e_value' => '1e-49',
'bit_score' => '196',
'alignment_length' => '933',
'identity_percentage' => '23.26',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'OS03G57300' => array(
'gene_id' => 'OS03G57300',
'e_value' => '1e-48',
'bit_score' => '193',
'alignment_length' => '748',
'identity_percentage' => '25.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'CR01G05390' => array(
'gene_id' => 'CR01G05390',
'e_value' => '1e-45',
'bit_score' => '184',
'alignment_length' => '1110',
'identity_percentage' => '21.89',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'VC00G45660' => array(
'gene_id' => 'VC00G45660',
'e_value' => '2e-40',
'bit_score' => '167',
'alignment_length' => '1140',
'identity_percentage' => '21.84',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'OL17G01190' => array(
'gene_id' => 'OL17G01190',
'e_value' => '3e-36',
'bit_score' => '153',
'alignment_length' => '646',
'identity_percentage' => '24.92',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'OM_18G01010' => array(
'gene_id' => 'OM_18G01010',
'e_value' => '1e-33',
'bit_score' => '145',
'alignment_length' => '587',
'identity_percentage' => '23.68',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'OT_18G01170' => array(
'gene_id' => 'OT_18G01170',
'e_value' => '6e-29',
'bit_score' => '130',
'alignment_length' => '591',
'identity_percentage' => '23.18',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_17G01190' => array(
'gene_id' => 'ORCC809_17G01190',
'e_value' => '6e-28',
'bit_score' => '126',
'alignment_length' => '902',
'identity_percentage' => '22.17',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'AP00G64240' => array(
'gene_id' => 'AP00G64240',
'e_value' => '3e-26',
'bit_score' => '120',
'alignment_length' => '373',
'identity_percentage' => '25.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'FBgn0260655' => array(
'gene_id' => 'FBgn0260655',
'e_value' => '1e-23',
'bit_score' => '112',
'alignment_length' => '617',
'identity_percentage' => '20.75',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_03G08000' => array(
'gene_id' => 'MRCC299_03G08000',
'e_value' => '9e-21',
'bit_score' => '103',
'alignment_length' => '831',
'identity_percentage' => '21.42',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_094G00020' => array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000033382' => array(
'gene_id' => 'ENSMUSG00000033382',
'e_value' => '4e-19',
'bit_score' => '98.2',
'alignment_length' => '438',
'identity_percentage' => '21.92',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'ENSG00000153339' => array(
'gene_id' => 'ENSG00000153339',
'e_value' => '1e-18',
'bit_score' => '96.7',
'alignment_length' => '355',
'identity_percentage' => '22.82',
'species' => 'hom',
'common_name' => 'Homo sapiens',
'gf' => array(
[maximum depth reached]
)
),
'MP17G02120' => array(
'gene_id' => 'MP17G02120',
'e_value' => '2e-17',
'bit_score' => '92.4',
'alignment_length' => '418',
'identity_percentage' => '24.16',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0292682' => array(
'gene_id' => 'DDB_G0292682',
'e_value' => '1e-15',
'bit_score' => '87.0',
'alignment_length' => '637',
'identity_percentage' => '20.25',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'PTI_21G02570' => array(
'gene_id' => 'PTI_21G02570',
'e_value' => '9e-15',
'bit_score' => '84.0',
'alignment_length' => '350',
'identity_percentage' => '24.29',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'WBGene00018512' => array(
'gene_id' => 'WBGene00018512',
'e_value' => '2e-12',
'bit_score' => '75.9',
'alignment_length' => '487',
'identity_percentage' => '23.00',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
[maximum depth reached]
)
),
'phs344240' => array(
'gene_id' => 'phs344240',
'e_value' => '9e-12',
'bit_score' => '73.9',
'alignment_length' => '290',
'identity_percentage' => '23.10',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_094G00010' => array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100001g67' => array(
'gene_id' => 'Naga_100001g67',
'e_value' => '6e-10',
'bit_score' => '68.2',
'alignment_length' => '347',
'identity_percentage' => '24.78',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'FC003G09000' => array(
'gene_id' => 'FC003G09000',
'e_value' => '4e-08',
'bit_score' => '62.0',
'alignment_length' => '360',
'identity_percentage' => '21.11',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'emh741120' => array(
'gene_id' => 'emh741120',
'e_value' => '3e-07',
'bit_score' => '59.3',
'alignment_length' => '614',
'identity_percentage' => '20.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'AA0024G00080' => array(
'gene_id' => 'AA0024G00080',
'e_value' => '1e-05',
'bit_score' => '54.3',
'alignment_length' => '117',
'identity_percentage' => '33.33',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'prcc4223' => array(
(int) 0 => 'RCC4223.05g02320'
),
'pse3' => array(
(int) 0 => 'PI00G14610'
),
'cvu' => array(
(int) 0 => 'CV00G05540'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_003G00300',
(int) 1 => 'CNC64A_003G00260'
),
'acg' => array(
(int) 0 => 'AC00G45200'
),
'ppa' => array(
(int) 0 => 'PP00270G00460'
),
'atr' => array(
(int) 0 => 'ATR_00030G00120'
),
'ath' => array(
(int) 0 => 'AT5G16280'
),
'osa' => array(
(int) 0 => 'OS03G57300'
),
'cre' => array(
(int) 0 => 'CR01G05390'
),
'vca' => array(
(int) 0 => 'VC00G45660'
),
'olu' => array(
(int) 0 => 'OL17G01190'
),
'ome' => array(
(int) 0 => 'OM_18G01010'
),
'ota' => array(
(int) 0 => 'OT_18G01170'
),
'orcc809' => array(
(int) 0 => 'ORCC809_17G01190'
),
'apr' => array(
(int) 0 => 'AP00G64240'
),
'drm' => array(
(int) 0 => 'FBgn0260655'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_03G08000'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000033382'
),
'hom' => array(
(int) 0 => 'ENSG00000153339'
),
'mpu' => array(
(int) 0 => 'MP17G02120'
),
'ddi' => array(
(int) 0 => 'DDB_G0292682'
),
'ptri' => array(
(int) 0 => 'PTI_21G02570'
),
'cel' => array(
(int) 0 => 'WBGene00018512'
),
'phs' => array(
(int) 0 => 'phs344240'
),
'nga' => array(
(int) 0 => 'Naga_100001g67'
),
'fcy' => array(
(int) 0 => 'FC003G09000'
),
'emh' => array(
(int) 0 => 'emh741120'
),
'aan' => array(
(int) 0 => 'AA0024G00080'
)
),
'gene_id' => 'RCC4223.05g02320',
'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' => 'RCC4223.05g02320',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'CM03G01680',
'gf_placeholder' => 'HOM03P014872',
'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(
'RCC4223.05g02320' => array(
'gene_id' => 'RCC4223.05g02320',
'e_value' => '0.0',
'bit_score' => '2335',
'alignment_length' => '1128',
'identity_percentage' => '100.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PI00G14610' => array(
'gene_id' => 'PI00G14610',
'e_value' => '0.0',
'bit_score' => '1986',
'alignment_length' => '1128',
'identity_percentage' => '84.93',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CV00G05540' => array(
'gene_id' => 'CV00G05540',
'e_value' => '4e-86',
'bit_score' => '309',
'alignment_length' => '1018',
'identity_percentage' => '26.72',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_003G00300' => array(
'gene_id' => 'CNC64A_003G00300',
'e_value' => '5e-70',
'bit_score' => '256',
'alignment_length' => '805',
'identity_percentage' => '27.58',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_003G00260' => array(
'gene_id' => 'CNC64A_003G00260',
'e_value' => '2e-69',
'bit_score' => '252',
'alignment_length' => '603',
'identity_percentage' => '30.18',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AC00G45200' => array(
'gene_id' => 'AC00G45200',
'e_value' => '8e-69',
'bit_score' => '253',
'alignment_length' => '954',
'identity_percentage' => '25.26',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PP00270G00460' => array(
'gene_id' => 'PP00270G00460',
'e_value' => '3e-53',
'bit_score' => '208',
'alignment_length' => '933',
'identity_percentage' => '24.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ATR_00030G00120' => array(
'gene_id' => 'ATR_00030G00120',
'e_value' => '4e-51',
'bit_score' => '201',
'alignment_length' => '842',
'identity_percentage' => '24.35',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AT5G16280' => array(
'gene_id' => 'AT5G16280',
'e_value' => '1e-49',
'bit_score' => '196',
'alignment_length' => '933',
'identity_percentage' => '23.26',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OS03G57300' => array(
'gene_id' => 'OS03G57300',
'e_value' => '1e-48',
'bit_score' => '193',
'alignment_length' => '748',
'identity_percentage' => '25.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CR01G05390' => array(
'gene_id' => 'CR01G05390',
'e_value' => '1e-45',
'bit_score' => '184',
'alignment_length' => '1110',
'identity_percentage' => '21.89',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'VC00G45660' => array(
'gene_id' => 'VC00G45660',
'e_value' => '2e-40',
'bit_score' => '167',
'alignment_length' => '1140',
'identity_percentage' => '21.84',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OL17G01190' => array(
'gene_id' => 'OL17G01190',
'e_value' => '3e-36',
'bit_score' => '153',
'alignment_length' => '646',
'identity_percentage' => '24.92',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OM_18G01010' => array(
'gene_id' => 'OM_18G01010',
'e_value' => '1e-33',
'bit_score' => '145',
'alignment_length' => '587',
'identity_percentage' => '23.68',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OT_18G01170' => array(
'gene_id' => 'OT_18G01170',
'e_value' => '6e-29',
'bit_score' => '130',
'alignment_length' => '591',
'identity_percentage' => '23.18',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ORCC809_17G01190' => array(
'gene_id' => 'ORCC809_17G01190',
'e_value' => '6e-28',
'bit_score' => '126',
'alignment_length' => '902',
'identity_percentage' => '22.17',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AP00G64240' => array(
'gene_id' => 'AP00G64240',
'e_value' => '3e-26',
'bit_score' => '120',
'alignment_length' => '373',
'identity_percentage' => '25.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'FBgn0260655' => array(
'gene_id' => 'FBgn0260655',
'e_value' => '1e-23',
'bit_score' => '112',
'alignment_length' => '617',
'identity_percentage' => '20.75',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'MRCC299_03G08000' => array(
'gene_id' => 'MRCC299_03G08000',
'e_value' => '9e-21',
'bit_score' => '103',
'alignment_length' => '831',
'identity_percentage' => '21.42',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_094G00020' => array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ENSMUSG00000033382' => array(
'gene_id' => 'ENSMUSG00000033382',
'e_value' => '4e-19',
'bit_score' => '98.2',
'alignment_length' => '438',
'identity_percentage' => '21.92',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ENSG00000153339' => array(
'gene_id' => 'ENSG00000153339',
'e_value' => '1e-18',
'bit_score' => '96.7',
'alignment_length' => '355',
'identity_percentage' => '22.82',
'species' => 'hom',
'common_name' => 'Homo sapiens',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'MP17G02120' => array(
'gene_id' => 'MP17G02120',
'e_value' => '2e-17',
'bit_score' => '92.4',
'alignment_length' => '418',
'identity_percentage' => '24.16',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'DDB_G0292682' => array(
'gene_id' => 'DDB_G0292682',
'e_value' => '1e-15',
'bit_score' => '87.0',
'alignment_length' => '637',
'identity_percentage' => '20.25',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PTI_21G02570' => array(
'gene_id' => 'PTI_21G02570',
'e_value' => '9e-15',
'bit_score' => '84.0',
'alignment_length' => '350',
'identity_percentage' => '24.29',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'WBGene00018512' => array(
'gene_id' => 'WBGene00018512',
'e_value' => '2e-12',
'bit_score' => '75.9',
'alignment_length' => '487',
'identity_percentage' => '23.00',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'phs344240' => array(
'gene_id' => 'phs344240',
'e_value' => '9e-12',
'bit_score' => '73.9',
'alignment_length' => '290',
'identity_percentage' => '23.10',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_094G00010' => array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'Naga_100001g67' => array(
'gene_id' => 'Naga_100001g67',
'e_value' => '6e-10',
'bit_score' => '68.2',
'alignment_length' => '347',
'identity_percentage' => '24.78',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'FC003G09000' => array(
'gene_id' => 'FC003G09000',
'e_value' => '4e-08',
'bit_score' => '62.0',
'alignment_length' => '360',
'identity_percentage' => '21.11',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'emh741120' => array(
'gene_id' => 'emh741120',
'e_value' => '3e-07',
'bit_score' => '59.3',
'alignment_length' => '614',
'identity_percentage' => '20.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P008886',
'ORTHOFAM' => 'ORTHO03P009063'
)
),
'AA0024G00080' => array(
'gene_id' => 'AA0024G00080',
'e_value' => '1e-05',
'bit_score' => '54.3',
'alignment_length' => '117',
'identity_percentage' => '33.33',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P034960',
'ORTHOFAM' => 'ORTHO03P034674'
)
)
)
$similarity_hits_species = array(
'prcc4223' => array(
(int) 0 => 'RCC4223.05g02320'
),
'pse3' => array(
(int) 0 => 'PI00G14610'
),
'cvu' => array(
(int) 0 => 'CV00G05540'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_003G00300',
(int) 1 => 'CNC64A_003G00260'
),
'acg' => array(
(int) 0 => 'AC00G45200'
),
'ppa' => array(
(int) 0 => 'PP00270G00460'
),
'atr' => array(
(int) 0 => 'ATR_00030G00120'
),
'ath' => array(
(int) 0 => 'AT5G16280'
),
'osa' => array(
(int) 0 => 'OS03G57300'
),
'cre' => array(
(int) 0 => 'CR01G05390'
),
'vca' => array(
(int) 0 => 'VC00G45660'
),
'olu' => array(
(int) 0 => 'OL17G01190'
),
'ome' => array(
(int) 0 => 'OM_18G01010'
),
'ota' => array(
(int) 0 => 'OT_18G01170'
),
'orcc809' => array(
(int) 0 => 'ORCC809_17G01190'
),
'apr' => array(
(int) 0 => 'AP00G64240'
),
'drm' => array(
(int) 0 => 'FBgn0260655'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_03G08000'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000033382'
),
'hom' => array(
(int) 0 => 'ENSG00000153339'
),
'mpu' => array(
(int) 0 => 'MP17G02120'
),
'ddi' => array(
(int) 0 => 'DDB_G0292682'
),
'ptri' => array(
(int) 0 => 'PTI_21G02570'
),
'cel' => array(
(int) 0 => 'WBGene00018512'
),
'phs' => array(
(int) 0 => 'phs344240'
),
'nga' => array(
(int) 0 => 'Naga_100001g67'
),
'fcy' => array(
(int) 0 => 'FC003G09000'
),
'emh' => array(
(int) 0 => 'emh741120'
),
'aan' => array(
(int) 0 => 'AA0024G00080'
)
)
$gene_id = 'RCC4223.05g02320'
$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 = 'RCC4223.05g02320'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'CM03G01680'
$gf_placeholder = 'HOM03P014872'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_094G00020'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146
Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]Code Context echo "<td><input type='checkbox' name='selected_genes[]' value='".$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(
'RCC4223.05g02320' => array(
'gene_id' => 'RCC4223.05g02320',
'e_value' => '0.0',
'bit_score' => '2335',
'alignment_length' => '1128',
'identity_percentage' => '100.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G14610' => array(
'gene_id' => 'PI00G14610',
'e_value' => '0.0',
'bit_score' => '1986',
'alignment_length' => '1128',
'identity_percentage' => '84.93',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'CV00G05540' => array(
'gene_id' => 'CV00G05540',
'e_value' => '4e-86',
'bit_score' => '309',
'alignment_length' => '1018',
'identity_percentage' => '26.72',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_003G00300' => array(
'gene_id' => 'CNC64A_003G00300',
'e_value' => '5e-70',
'bit_score' => '256',
'alignment_length' => '805',
'identity_percentage' => '27.58',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_003G00260' => array(
'gene_id' => 'CNC64A_003G00260',
'e_value' => '2e-69',
'bit_score' => '252',
'alignment_length' => '603',
'identity_percentage' => '30.18',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'AC00G45200' => array(
'gene_id' => 'AC00G45200',
'e_value' => '8e-69',
'bit_score' => '253',
'alignment_length' => '954',
'identity_percentage' => '25.26',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'PP00270G00460' => array(
'gene_id' => 'PP00270G00460',
'e_value' => '3e-53',
'bit_score' => '208',
'alignment_length' => '933',
'identity_percentage' => '24.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00030G00120' => array(
'gene_id' => 'ATR_00030G00120',
'e_value' => '4e-51',
'bit_score' => '201',
'alignment_length' => '842',
'identity_percentage' => '24.35',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'AT5G16280' => array(
'gene_id' => 'AT5G16280',
'e_value' => '1e-49',
'bit_score' => '196',
'alignment_length' => '933',
'identity_percentage' => '23.26',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'OS03G57300' => array(
'gene_id' => 'OS03G57300',
'e_value' => '1e-48',
'bit_score' => '193',
'alignment_length' => '748',
'identity_percentage' => '25.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'CR01G05390' => array(
'gene_id' => 'CR01G05390',
'e_value' => '1e-45',
'bit_score' => '184',
'alignment_length' => '1110',
'identity_percentage' => '21.89',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'VC00G45660' => array(
'gene_id' => 'VC00G45660',
'e_value' => '2e-40',
'bit_score' => '167',
'alignment_length' => '1140',
'identity_percentage' => '21.84',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'OL17G01190' => array(
'gene_id' => 'OL17G01190',
'e_value' => '3e-36',
'bit_score' => '153',
'alignment_length' => '646',
'identity_percentage' => '24.92',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'OM_18G01010' => array(
'gene_id' => 'OM_18G01010',
'e_value' => '1e-33',
'bit_score' => '145',
'alignment_length' => '587',
'identity_percentage' => '23.68',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'OT_18G01170' => array(
'gene_id' => 'OT_18G01170',
'e_value' => '6e-29',
'bit_score' => '130',
'alignment_length' => '591',
'identity_percentage' => '23.18',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_17G01190' => array(
'gene_id' => 'ORCC809_17G01190',
'e_value' => '6e-28',
'bit_score' => '126',
'alignment_length' => '902',
'identity_percentage' => '22.17',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'AP00G64240' => array(
'gene_id' => 'AP00G64240',
'e_value' => '3e-26',
'bit_score' => '120',
'alignment_length' => '373',
'identity_percentage' => '25.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'FBgn0260655' => array(
'gene_id' => 'FBgn0260655',
'e_value' => '1e-23',
'bit_score' => '112',
'alignment_length' => '617',
'identity_percentage' => '20.75',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_03G08000' => array(
'gene_id' => 'MRCC299_03G08000',
'e_value' => '9e-21',
'bit_score' => '103',
'alignment_length' => '831',
'identity_percentage' => '21.42',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_094G00020' => array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000033382' => array(
'gene_id' => 'ENSMUSG00000033382',
'e_value' => '4e-19',
'bit_score' => '98.2',
'alignment_length' => '438',
'identity_percentage' => '21.92',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'ENSG00000153339' => array(
'gene_id' => 'ENSG00000153339',
'e_value' => '1e-18',
'bit_score' => '96.7',
'alignment_length' => '355',
'identity_percentage' => '22.82',
'species' => 'hom',
'common_name' => 'Homo sapiens',
'gf' => array(
[maximum depth reached]
)
),
'MP17G02120' => array(
'gene_id' => 'MP17G02120',
'e_value' => '2e-17',
'bit_score' => '92.4',
'alignment_length' => '418',
'identity_percentage' => '24.16',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0292682' => array(
'gene_id' => 'DDB_G0292682',
'e_value' => '1e-15',
'bit_score' => '87.0',
'alignment_length' => '637',
'identity_percentage' => '20.25',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'PTI_21G02570' => array(
'gene_id' => 'PTI_21G02570',
'e_value' => '9e-15',
'bit_score' => '84.0',
'alignment_length' => '350',
'identity_percentage' => '24.29',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'WBGene00018512' => array(
'gene_id' => 'WBGene00018512',
'e_value' => '2e-12',
'bit_score' => '75.9',
'alignment_length' => '487',
'identity_percentage' => '23.00',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
[maximum depth reached]
)
),
'phs344240' => array(
'gene_id' => 'phs344240',
'e_value' => '9e-12',
'bit_score' => '73.9',
'alignment_length' => '290',
'identity_percentage' => '23.10',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_094G00010' => array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100001g67' => array(
'gene_id' => 'Naga_100001g67',
'e_value' => '6e-10',
'bit_score' => '68.2',
'alignment_length' => '347',
'identity_percentage' => '24.78',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'FC003G09000' => array(
'gene_id' => 'FC003G09000',
'e_value' => '4e-08',
'bit_score' => '62.0',
'alignment_length' => '360',
'identity_percentage' => '21.11',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'emh741120' => array(
'gene_id' => 'emh741120',
'e_value' => '3e-07',
'bit_score' => '59.3',
'alignment_length' => '614',
'identity_percentage' => '20.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'AA0024G00080' => array(
'gene_id' => 'AA0024G00080',
'e_value' => '1e-05',
'bit_score' => '54.3',
'alignment_length' => '117',
'identity_percentage' => '33.33',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'prcc4223' => array(
(int) 0 => 'RCC4223.05g02320'
),
'pse3' => array(
(int) 0 => 'PI00G14610'
),
'cvu' => array(
(int) 0 => 'CV00G05540'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_003G00300',
(int) 1 => 'CNC64A_003G00260'
),
'acg' => array(
(int) 0 => 'AC00G45200'
),
'ppa' => array(
(int) 0 => 'PP00270G00460'
),
'atr' => array(
(int) 0 => 'ATR_00030G00120'
),
'ath' => array(
(int) 0 => 'AT5G16280'
),
'osa' => array(
(int) 0 => 'OS03G57300'
),
'cre' => array(
(int) 0 => 'CR01G05390'
),
'vca' => array(
(int) 0 => 'VC00G45660'
),
'olu' => array(
(int) 0 => 'OL17G01190'
),
'ome' => array(
(int) 0 => 'OM_18G01010'
),
'ota' => array(
(int) 0 => 'OT_18G01170'
),
'orcc809' => array(
(int) 0 => 'ORCC809_17G01190'
),
'apr' => array(
(int) 0 => 'AP00G64240'
),
'drm' => array(
(int) 0 => 'FBgn0260655'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_03G08000'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000033382'
),
'hom' => array(
(int) 0 => 'ENSG00000153339'
),
'mpu' => array(
(int) 0 => 'MP17G02120'
),
'ddi' => array(
(int) 0 => 'DDB_G0292682'
),
'ptri' => array(
(int) 0 => 'PTI_21G02570'
),
'cel' => array(
(int) 0 => 'WBGene00018512'
),
'phs' => array(
(int) 0 => 'phs344240'
),
'nga' => array(
(int) 0 => 'Naga_100001g67'
),
'fcy' => array(
(int) 0 => 'FC003G09000'
),
'emh' => array(
(int) 0 => 'emh741120'
),
'aan' => array(
(int) 0 => 'AA0024G00080'
)
),
'gene_id' => 'RCC4223.05g02320',
'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' => 'RCC4223.05g02320',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'CM03G01680',
'gf_placeholder' => 'HOM03P014872',
'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(
'RCC4223.05g02320' => array(
'gene_id' => 'RCC4223.05g02320',
'e_value' => '0.0',
'bit_score' => '2335',
'alignment_length' => '1128',
'identity_percentage' => '100.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PI00G14610' => array(
'gene_id' => 'PI00G14610',
'e_value' => '0.0',
'bit_score' => '1986',
'alignment_length' => '1128',
'identity_percentage' => '84.93',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CV00G05540' => array(
'gene_id' => 'CV00G05540',
'e_value' => '4e-86',
'bit_score' => '309',
'alignment_length' => '1018',
'identity_percentage' => '26.72',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_003G00300' => array(
'gene_id' => 'CNC64A_003G00300',
'e_value' => '5e-70',
'bit_score' => '256',
'alignment_length' => '805',
'identity_percentage' => '27.58',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_003G00260' => array(
'gene_id' => 'CNC64A_003G00260',
'e_value' => '2e-69',
'bit_score' => '252',
'alignment_length' => '603',
'identity_percentage' => '30.18',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AC00G45200' => array(
'gene_id' => 'AC00G45200',
'e_value' => '8e-69',
'bit_score' => '253',
'alignment_length' => '954',
'identity_percentage' => '25.26',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PP00270G00460' => array(
'gene_id' => 'PP00270G00460',
'e_value' => '3e-53',
'bit_score' => '208',
'alignment_length' => '933',
'identity_percentage' => '24.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ATR_00030G00120' => array(
'gene_id' => 'ATR_00030G00120',
'e_value' => '4e-51',
'bit_score' => '201',
'alignment_length' => '842',
'identity_percentage' => '24.35',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AT5G16280' => array(
'gene_id' => 'AT5G16280',
'e_value' => '1e-49',
'bit_score' => '196',
'alignment_length' => '933',
'identity_percentage' => '23.26',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OS03G57300' => array(
'gene_id' => 'OS03G57300',
'e_value' => '1e-48',
'bit_score' => '193',
'alignment_length' => '748',
'identity_percentage' => '25.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CR01G05390' => array(
'gene_id' => 'CR01G05390',
'e_value' => '1e-45',
'bit_score' => '184',
'alignment_length' => '1110',
'identity_percentage' => '21.89',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'VC00G45660' => array(
'gene_id' => 'VC00G45660',
'e_value' => '2e-40',
'bit_score' => '167',
'alignment_length' => '1140',
'identity_percentage' => '21.84',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OL17G01190' => array(
'gene_id' => 'OL17G01190',
'e_value' => '3e-36',
'bit_score' => '153',
'alignment_length' => '646',
'identity_percentage' => '24.92',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OM_18G01010' => array(
'gene_id' => 'OM_18G01010',
'e_value' => '1e-33',
'bit_score' => '145',
'alignment_length' => '587',
'identity_percentage' => '23.68',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OT_18G01170' => array(
'gene_id' => 'OT_18G01170',
'e_value' => '6e-29',
'bit_score' => '130',
'alignment_length' => '591',
'identity_percentage' => '23.18',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ORCC809_17G01190' => array(
'gene_id' => 'ORCC809_17G01190',
'e_value' => '6e-28',
'bit_score' => '126',
'alignment_length' => '902',
'identity_percentage' => '22.17',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AP00G64240' => array(
'gene_id' => 'AP00G64240',
'e_value' => '3e-26',
'bit_score' => '120',
'alignment_length' => '373',
'identity_percentage' => '25.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'FBgn0260655' => array(
'gene_id' => 'FBgn0260655',
'e_value' => '1e-23',
'bit_score' => '112',
'alignment_length' => '617',
'identity_percentage' => '20.75',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'MRCC299_03G08000' => array(
'gene_id' => 'MRCC299_03G08000',
'e_value' => '9e-21',
'bit_score' => '103',
'alignment_length' => '831',
'identity_percentage' => '21.42',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_094G00020' => array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ENSMUSG00000033382' => array(
'gene_id' => 'ENSMUSG00000033382',
'e_value' => '4e-19',
'bit_score' => '98.2',
'alignment_length' => '438',
'identity_percentage' => '21.92',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ENSG00000153339' => array(
'gene_id' => 'ENSG00000153339',
'e_value' => '1e-18',
'bit_score' => '96.7',
'alignment_length' => '355',
'identity_percentage' => '22.82',
'species' => 'hom',
'common_name' => 'Homo sapiens',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'MP17G02120' => array(
'gene_id' => 'MP17G02120',
'e_value' => '2e-17',
'bit_score' => '92.4',
'alignment_length' => '418',
'identity_percentage' => '24.16',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'DDB_G0292682' => array(
'gene_id' => 'DDB_G0292682',
'e_value' => '1e-15',
'bit_score' => '87.0',
'alignment_length' => '637',
'identity_percentage' => '20.25',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PTI_21G02570' => array(
'gene_id' => 'PTI_21G02570',
'e_value' => '9e-15',
'bit_score' => '84.0',
'alignment_length' => '350',
'identity_percentage' => '24.29',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'WBGene00018512' => array(
'gene_id' => 'WBGene00018512',
'e_value' => '2e-12',
'bit_score' => '75.9',
'alignment_length' => '487',
'identity_percentage' => '23.00',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'phs344240' => array(
'gene_id' => 'phs344240',
'e_value' => '9e-12',
'bit_score' => '73.9',
'alignment_length' => '290',
'identity_percentage' => '23.10',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_094G00010' => array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'Naga_100001g67' => array(
'gene_id' => 'Naga_100001g67',
'e_value' => '6e-10',
'bit_score' => '68.2',
'alignment_length' => '347',
'identity_percentage' => '24.78',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'FC003G09000' => array(
'gene_id' => 'FC003G09000',
'e_value' => '4e-08',
'bit_score' => '62.0',
'alignment_length' => '360',
'identity_percentage' => '21.11',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'emh741120' => array(
'gene_id' => 'emh741120',
'e_value' => '3e-07',
'bit_score' => '59.3',
'alignment_length' => '614',
'identity_percentage' => '20.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P008886',
'ORTHOFAM' => 'ORTHO03P009063'
)
),
'AA0024G00080' => array(
'gene_id' => 'AA0024G00080',
'e_value' => '1e-05',
'bit_score' => '54.3',
'alignment_length' => '117',
'identity_percentage' => '33.33',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P034960',
'ORTHOFAM' => 'ORTHO03P034674'
)
)
)
$similarity_hits_species = array(
'prcc4223' => array(
(int) 0 => 'RCC4223.05g02320'
),
'pse3' => array(
(int) 0 => 'PI00G14610'
),
'cvu' => array(
(int) 0 => 'CV00G05540'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_003G00300',
(int) 1 => 'CNC64A_003G00260'
),
'acg' => array(
(int) 0 => 'AC00G45200'
),
'ppa' => array(
(int) 0 => 'PP00270G00460'
),
'atr' => array(
(int) 0 => 'ATR_00030G00120'
),
'ath' => array(
(int) 0 => 'AT5G16280'
),
'osa' => array(
(int) 0 => 'OS03G57300'
),
'cre' => array(
(int) 0 => 'CR01G05390'
),
'vca' => array(
(int) 0 => 'VC00G45660'
),
'olu' => array(
(int) 0 => 'OL17G01190'
),
'ome' => array(
(int) 0 => 'OM_18G01010'
),
'ota' => array(
(int) 0 => 'OT_18G01170'
),
'orcc809' => array(
(int) 0 => 'ORCC809_17G01190'
),
'apr' => array(
(int) 0 => 'AP00G64240'
),
'drm' => array(
(int) 0 => 'FBgn0260655'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_03G08000'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000033382'
),
'hom' => array(
(int) 0 => 'ENSG00000153339'
),
'mpu' => array(
(int) 0 => 'MP17G02120'
),
'ddi' => array(
(int) 0 => 'DDB_G0292682'
),
'ptri' => array(
(int) 0 => 'PTI_21G02570'
),
'cel' => array(
(int) 0 => 'WBGene00018512'
),
'phs' => array(
(int) 0 => 'phs344240'
),
'nga' => array(
(int) 0 => 'Naga_100001g67'
),
'fcy' => array(
(int) 0 => 'FC003G09000'
),
'emh' => array(
(int) 0 => 'emh741120'
),
'aan' => array(
(int) 0 => 'AA0024G00080'
)
)
$gene_id = 'RCC4223.05g02320'
$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 = 'RCC4223.05g02320'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'CM03G01680'
$gf_placeholder = 'HOM03P014872'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_094G00020'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146
|
3e-19 |
94.4 |
158 |
38.61 |
|
CNC64A_094G00010 |
Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]Code Context echo "<td><input type='checkbox' name='selected_genes[]' value='".$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(
'RCC4223.05g02320' => array(
'gene_id' => 'RCC4223.05g02320',
'e_value' => '0.0',
'bit_score' => '2335',
'alignment_length' => '1128',
'identity_percentage' => '100.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G14610' => array(
'gene_id' => 'PI00G14610',
'e_value' => '0.0',
'bit_score' => '1986',
'alignment_length' => '1128',
'identity_percentage' => '84.93',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'CV00G05540' => array(
'gene_id' => 'CV00G05540',
'e_value' => '4e-86',
'bit_score' => '309',
'alignment_length' => '1018',
'identity_percentage' => '26.72',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_003G00300' => array(
'gene_id' => 'CNC64A_003G00300',
'e_value' => '5e-70',
'bit_score' => '256',
'alignment_length' => '805',
'identity_percentage' => '27.58',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_003G00260' => array(
'gene_id' => 'CNC64A_003G00260',
'e_value' => '2e-69',
'bit_score' => '252',
'alignment_length' => '603',
'identity_percentage' => '30.18',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'AC00G45200' => array(
'gene_id' => 'AC00G45200',
'e_value' => '8e-69',
'bit_score' => '253',
'alignment_length' => '954',
'identity_percentage' => '25.26',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'PP00270G00460' => array(
'gene_id' => 'PP00270G00460',
'e_value' => '3e-53',
'bit_score' => '208',
'alignment_length' => '933',
'identity_percentage' => '24.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00030G00120' => array(
'gene_id' => 'ATR_00030G00120',
'e_value' => '4e-51',
'bit_score' => '201',
'alignment_length' => '842',
'identity_percentage' => '24.35',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'AT5G16280' => array(
'gene_id' => 'AT5G16280',
'e_value' => '1e-49',
'bit_score' => '196',
'alignment_length' => '933',
'identity_percentage' => '23.26',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'OS03G57300' => array(
'gene_id' => 'OS03G57300',
'e_value' => '1e-48',
'bit_score' => '193',
'alignment_length' => '748',
'identity_percentage' => '25.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'CR01G05390' => array(
'gene_id' => 'CR01G05390',
'e_value' => '1e-45',
'bit_score' => '184',
'alignment_length' => '1110',
'identity_percentage' => '21.89',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'VC00G45660' => array(
'gene_id' => 'VC00G45660',
'e_value' => '2e-40',
'bit_score' => '167',
'alignment_length' => '1140',
'identity_percentage' => '21.84',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'OL17G01190' => array(
'gene_id' => 'OL17G01190',
'e_value' => '3e-36',
'bit_score' => '153',
'alignment_length' => '646',
'identity_percentage' => '24.92',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'OM_18G01010' => array(
'gene_id' => 'OM_18G01010',
'e_value' => '1e-33',
'bit_score' => '145',
'alignment_length' => '587',
'identity_percentage' => '23.68',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'OT_18G01170' => array(
'gene_id' => 'OT_18G01170',
'e_value' => '6e-29',
'bit_score' => '130',
'alignment_length' => '591',
'identity_percentage' => '23.18',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_17G01190' => array(
'gene_id' => 'ORCC809_17G01190',
'e_value' => '6e-28',
'bit_score' => '126',
'alignment_length' => '902',
'identity_percentage' => '22.17',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'AP00G64240' => array(
'gene_id' => 'AP00G64240',
'e_value' => '3e-26',
'bit_score' => '120',
'alignment_length' => '373',
'identity_percentage' => '25.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'FBgn0260655' => array(
'gene_id' => 'FBgn0260655',
'e_value' => '1e-23',
'bit_score' => '112',
'alignment_length' => '617',
'identity_percentage' => '20.75',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_03G08000' => array(
'gene_id' => 'MRCC299_03G08000',
'e_value' => '9e-21',
'bit_score' => '103',
'alignment_length' => '831',
'identity_percentage' => '21.42',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_094G00020' => array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000033382' => array(
'gene_id' => 'ENSMUSG00000033382',
'e_value' => '4e-19',
'bit_score' => '98.2',
'alignment_length' => '438',
'identity_percentage' => '21.92',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'ENSG00000153339' => array(
'gene_id' => 'ENSG00000153339',
'e_value' => '1e-18',
'bit_score' => '96.7',
'alignment_length' => '355',
'identity_percentage' => '22.82',
'species' => 'hom',
'common_name' => 'Homo sapiens',
'gf' => array(
[maximum depth reached]
)
),
'MP17G02120' => array(
'gene_id' => 'MP17G02120',
'e_value' => '2e-17',
'bit_score' => '92.4',
'alignment_length' => '418',
'identity_percentage' => '24.16',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0292682' => array(
'gene_id' => 'DDB_G0292682',
'e_value' => '1e-15',
'bit_score' => '87.0',
'alignment_length' => '637',
'identity_percentage' => '20.25',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'PTI_21G02570' => array(
'gene_id' => 'PTI_21G02570',
'e_value' => '9e-15',
'bit_score' => '84.0',
'alignment_length' => '350',
'identity_percentage' => '24.29',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'WBGene00018512' => array(
'gene_id' => 'WBGene00018512',
'e_value' => '2e-12',
'bit_score' => '75.9',
'alignment_length' => '487',
'identity_percentage' => '23.00',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
[maximum depth reached]
)
),
'phs344240' => array(
'gene_id' => 'phs344240',
'e_value' => '9e-12',
'bit_score' => '73.9',
'alignment_length' => '290',
'identity_percentage' => '23.10',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_094G00010' => array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100001g67' => array(
'gene_id' => 'Naga_100001g67',
'e_value' => '6e-10',
'bit_score' => '68.2',
'alignment_length' => '347',
'identity_percentage' => '24.78',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'FC003G09000' => array(
'gene_id' => 'FC003G09000',
'e_value' => '4e-08',
'bit_score' => '62.0',
'alignment_length' => '360',
'identity_percentage' => '21.11',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'emh741120' => array(
'gene_id' => 'emh741120',
'e_value' => '3e-07',
'bit_score' => '59.3',
'alignment_length' => '614',
'identity_percentage' => '20.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'AA0024G00080' => array(
'gene_id' => 'AA0024G00080',
'e_value' => '1e-05',
'bit_score' => '54.3',
'alignment_length' => '117',
'identity_percentage' => '33.33',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'prcc4223' => array(
(int) 0 => 'RCC4223.05g02320'
),
'pse3' => array(
(int) 0 => 'PI00G14610'
),
'cvu' => array(
(int) 0 => 'CV00G05540'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_003G00300',
(int) 1 => 'CNC64A_003G00260'
),
'acg' => array(
(int) 0 => 'AC00G45200'
),
'ppa' => array(
(int) 0 => 'PP00270G00460'
),
'atr' => array(
(int) 0 => 'ATR_00030G00120'
),
'ath' => array(
(int) 0 => 'AT5G16280'
),
'osa' => array(
(int) 0 => 'OS03G57300'
),
'cre' => array(
(int) 0 => 'CR01G05390'
),
'vca' => array(
(int) 0 => 'VC00G45660'
),
'olu' => array(
(int) 0 => 'OL17G01190'
),
'ome' => array(
(int) 0 => 'OM_18G01010'
),
'ota' => array(
(int) 0 => 'OT_18G01170'
),
'orcc809' => array(
(int) 0 => 'ORCC809_17G01190'
),
'apr' => array(
(int) 0 => 'AP00G64240'
),
'drm' => array(
(int) 0 => 'FBgn0260655'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_03G08000'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000033382'
),
'hom' => array(
(int) 0 => 'ENSG00000153339'
),
'mpu' => array(
(int) 0 => 'MP17G02120'
),
'ddi' => array(
(int) 0 => 'DDB_G0292682'
),
'ptri' => array(
(int) 0 => 'PTI_21G02570'
),
'cel' => array(
(int) 0 => 'WBGene00018512'
),
'phs' => array(
(int) 0 => 'phs344240'
),
'nga' => array(
(int) 0 => 'Naga_100001g67'
),
'fcy' => array(
(int) 0 => 'FC003G09000'
),
'emh' => array(
(int) 0 => 'emh741120'
),
'aan' => array(
(int) 0 => 'AA0024G00080'
)
),
'gene_id' => 'RCC4223.05g02320',
'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' => 'RCC4223.05g02320',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'CM03G01680',
'gf_placeholder' => 'HOM03P014872',
'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(
'RCC4223.05g02320' => array(
'gene_id' => 'RCC4223.05g02320',
'e_value' => '0.0',
'bit_score' => '2335',
'alignment_length' => '1128',
'identity_percentage' => '100.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PI00G14610' => array(
'gene_id' => 'PI00G14610',
'e_value' => '0.0',
'bit_score' => '1986',
'alignment_length' => '1128',
'identity_percentage' => '84.93',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CV00G05540' => array(
'gene_id' => 'CV00G05540',
'e_value' => '4e-86',
'bit_score' => '309',
'alignment_length' => '1018',
'identity_percentage' => '26.72',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_003G00300' => array(
'gene_id' => 'CNC64A_003G00300',
'e_value' => '5e-70',
'bit_score' => '256',
'alignment_length' => '805',
'identity_percentage' => '27.58',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_003G00260' => array(
'gene_id' => 'CNC64A_003G00260',
'e_value' => '2e-69',
'bit_score' => '252',
'alignment_length' => '603',
'identity_percentage' => '30.18',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AC00G45200' => array(
'gene_id' => 'AC00G45200',
'e_value' => '8e-69',
'bit_score' => '253',
'alignment_length' => '954',
'identity_percentage' => '25.26',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PP00270G00460' => array(
'gene_id' => 'PP00270G00460',
'e_value' => '3e-53',
'bit_score' => '208',
'alignment_length' => '933',
'identity_percentage' => '24.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ATR_00030G00120' => array(
'gene_id' => 'ATR_00030G00120',
'e_value' => '4e-51',
'bit_score' => '201',
'alignment_length' => '842',
'identity_percentage' => '24.35',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AT5G16280' => array(
'gene_id' => 'AT5G16280',
'e_value' => '1e-49',
'bit_score' => '196',
'alignment_length' => '933',
'identity_percentage' => '23.26',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OS03G57300' => array(
'gene_id' => 'OS03G57300',
'e_value' => '1e-48',
'bit_score' => '193',
'alignment_length' => '748',
'identity_percentage' => '25.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CR01G05390' => array(
'gene_id' => 'CR01G05390',
'e_value' => '1e-45',
'bit_score' => '184',
'alignment_length' => '1110',
'identity_percentage' => '21.89',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'VC00G45660' => array(
'gene_id' => 'VC00G45660',
'e_value' => '2e-40',
'bit_score' => '167',
'alignment_length' => '1140',
'identity_percentage' => '21.84',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OL17G01190' => array(
'gene_id' => 'OL17G01190',
'e_value' => '3e-36',
'bit_score' => '153',
'alignment_length' => '646',
'identity_percentage' => '24.92',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OM_18G01010' => array(
'gene_id' => 'OM_18G01010',
'e_value' => '1e-33',
'bit_score' => '145',
'alignment_length' => '587',
'identity_percentage' => '23.68',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OT_18G01170' => array(
'gene_id' => 'OT_18G01170',
'e_value' => '6e-29',
'bit_score' => '130',
'alignment_length' => '591',
'identity_percentage' => '23.18',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ORCC809_17G01190' => array(
'gene_id' => 'ORCC809_17G01190',
'e_value' => '6e-28',
'bit_score' => '126',
'alignment_length' => '902',
'identity_percentage' => '22.17',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AP00G64240' => array(
'gene_id' => 'AP00G64240',
'e_value' => '3e-26',
'bit_score' => '120',
'alignment_length' => '373',
'identity_percentage' => '25.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'FBgn0260655' => array(
'gene_id' => 'FBgn0260655',
'e_value' => '1e-23',
'bit_score' => '112',
'alignment_length' => '617',
'identity_percentage' => '20.75',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'MRCC299_03G08000' => array(
'gene_id' => 'MRCC299_03G08000',
'e_value' => '9e-21',
'bit_score' => '103',
'alignment_length' => '831',
'identity_percentage' => '21.42',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_094G00020' => array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ENSMUSG00000033382' => array(
'gene_id' => 'ENSMUSG00000033382',
'e_value' => '4e-19',
'bit_score' => '98.2',
'alignment_length' => '438',
'identity_percentage' => '21.92',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ENSG00000153339' => array(
'gene_id' => 'ENSG00000153339',
'e_value' => '1e-18',
'bit_score' => '96.7',
'alignment_length' => '355',
'identity_percentage' => '22.82',
'species' => 'hom',
'common_name' => 'Homo sapiens',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'MP17G02120' => array(
'gene_id' => 'MP17G02120',
'e_value' => '2e-17',
'bit_score' => '92.4',
'alignment_length' => '418',
'identity_percentage' => '24.16',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'DDB_G0292682' => array(
'gene_id' => 'DDB_G0292682',
'e_value' => '1e-15',
'bit_score' => '87.0',
'alignment_length' => '637',
'identity_percentage' => '20.25',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PTI_21G02570' => array(
'gene_id' => 'PTI_21G02570',
'e_value' => '9e-15',
'bit_score' => '84.0',
'alignment_length' => '350',
'identity_percentage' => '24.29',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'WBGene00018512' => array(
'gene_id' => 'WBGene00018512',
'e_value' => '2e-12',
'bit_score' => '75.9',
'alignment_length' => '487',
'identity_percentage' => '23.00',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'phs344240' => array(
'gene_id' => 'phs344240',
'e_value' => '9e-12',
'bit_score' => '73.9',
'alignment_length' => '290',
'identity_percentage' => '23.10',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_094G00010' => array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'Naga_100001g67' => array(
'gene_id' => 'Naga_100001g67',
'e_value' => '6e-10',
'bit_score' => '68.2',
'alignment_length' => '347',
'identity_percentage' => '24.78',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'FC003G09000' => array(
'gene_id' => 'FC003G09000',
'e_value' => '4e-08',
'bit_score' => '62.0',
'alignment_length' => '360',
'identity_percentage' => '21.11',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'emh741120' => array(
'gene_id' => 'emh741120',
'e_value' => '3e-07',
'bit_score' => '59.3',
'alignment_length' => '614',
'identity_percentage' => '20.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P008886',
'ORTHOFAM' => 'ORTHO03P009063'
)
),
'AA0024G00080' => array(
'gene_id' => 'AA0024G00080',
'e_value' => '1e-05',
'bit_score' => '54.3',
'alignment_length' => '117',
'identity_percentage' => '33.33',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P034960',
'ORTHOFAM' => 'ORTHO03P034674'
)
)
)
$similarity_hits_species = array(
'prcc4223' => array(
(int) 0 => 'RCC4223.05g02320'
),
'pse3' => array(
(int) 0 => 'PI00G14610'
),
'cvu' => array(
(int) 0 => 'CV00G05540'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_003G00300',
(int) 1 => 'CNC64A_003G00260'
),
'acg' => array(
(int) 0 => 'AC00G45200'
),
'ppa' => array(
(int) 0 => 'PP00270G00460'
),
'atr' => array(
(int) 0 => 'ATR_00030G00120'
),
'ath' => array(
(int) 0 => 'AT5G16280'
),
'osa' => array(
(int) 0 => 'OS03G57300'
),
'cre' => array(
(int) 0 => 'CR01G05390'
),
'vca' => array(
(int) 0 => 'VC00G45660'
),
'olu' => array(
(int) 0 => 'OL17G01190'
),
'ome' => array(
(int) 0 => 'OM_18G01010'
),
'ota' => array(
(int) 0 => 'OT_18G01170'
),
'orcc809' => array(
(int) 0 => 'ORCC809_17G01190'
),
'apr' => array(
(int) 0 => 'AP00G64240'
),
'drm' => array(
(int) 0 => 'FBgn0260655'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_03G08000'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000033382'
),
'hom' => array(
(int) 0 => 'ENSG00000153339'
),
'mpu' => array(
(int) 0 => 'MP17G02120'
),
'ddi' => array(
(int) 0 => 'DDB_G0292682'
),
'ptri' => array(
(int) 0 => 'PTI_21G02570'
),
'cel' => array(
(int) 0 => 'WBGene00018512'
),
'phs' => array(
(int) 0 => 'phs344240'
),
'nga' => array(
(int) 0 => 'Naga_100001g67'
),
'fcy' => array(
(int) 0 => 'FC003G09000'
),
'emh' => array(
(int) 0 => 'emh741120'
),
'aan' => array(
(int) 0 => 'AA0024G00080'
)
)
$gene_id = 'RCC4223.05g02320'
$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 = 'RCC4223.05g02320'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'CM03G01680'
$gf_placeholder = 'HOM03P014872'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_094G00010'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146
Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]Code Context echo "<td><input type='checkbox' name='selected_genes[]' value='".$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(
'RCC4223.05g02320' => array(
'gene_id' => 'RCC4223.05g02320',
'e_value' => '0.0',
'bit_score' => '2335',
'alignment_length' => '1128',
'identity_percentage' => '100.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G14610' => array(
'gene_id' => 'PI00G14610',
'e_value' => '0.0',
'bit_score' => '1986',
'alignment_length' => '1128',
'identity_percentage' => '84.93',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'CV00G05540' => array(
'gene_id' => 'CV00G05540',
'e_value' => '4e-86',
'bit_score' => '309',
'alignment_length' => '1018',
'identity_percentage' => '26.72',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_003G00300' => array(
'gene_id' => 'CNC64A_003G00300',
'e_value' => '5e-70',
'bit_score' => '256',
'alignment_length' => '805',
'identity_percentage' => '27.58',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_003G00260' => array(
'gene_id' => 'CNC64A_003G00260',
'e_value' => '2e-69',
'bit_score' => '252',
'alignment_length' => '603',
'identity_percentage' => '30.18',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'AC00G45200' => array(
'gene_id' => 'AC00G45200',
'e_value' => '8e-69',
'bit_score' => '253',
'alignment_length' => '954',
'identity_percentage' => '25.26',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'PP00270G00460' => array(
'gene_id' => 'PP00270G00460',
'e_value' => '3e-53',
'bit_score' => '208',
'alignment_length' => '933',
'identity_percentage' => '24.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00030G00120' => array(
'gene_id' => 'ATR_00030G00120',
'e_value' => '4e-51',
'bit_score' => '201',
'alignment_length' => '842',
'identity_percentage' => '24.35',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'AT5G16280' => array(
'gene_id' => 'AT5G16280',
'e_value' => '1e-49',
'bit_score' => '196',
'alignment_length' => '933',
'identity_percentage' => '23.26',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'OS03G57300' => array(
'gene_id' => 'OS03G57300',
'e_value' => '1e-48',
'bit_score' => '193',
'alignment_length' => '748',
'identity_percentage' => '25.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'CR01G05390' => array(
'gene_id' => 'CR01G05390',
'e_value' => '1e-45',
'bit_score' => '184',
'alignment_length' => '1110',
'identity_percentage' => '21.89',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'VC00G45660' => array(
'gene_id' => 'VC00G45660',
'e_value' => '2e-40',
'bit_score' => '167',
'alignment_length' => '1140',
'identity_percentage' => '21.84',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'OL17G01190' => array(
'gene_id' => 'OL17G01190',
'e_value' => '3e-36',
'bit_score' => '153',
'alignment_length' => '646',
'identity_percentage' => '24.92',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'OM_18G01010' => array(
'gene_id' => 'OM_18G01010',
'e_value' => '1e-33',
'bit_score' => '145',
'alignment_length' => '587',
'identity_percentage' => '23.68',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'OT_18G01170' => array(
'gene_id' => 'OT_18G01170',
'e_value' => '6e-29',
'bit_score' => '130',
'alignment_length' => '591',
'identity_percentage' => '23.18',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_17G01190' => array(
'gene_id' => 'ORCC809_17G01190',
'e_value' => '6e-28',
'bit_score' => '126',
'alignment_length' => '902',
'identity_percentage' => '22.17',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'AP00G64240' => array(
'gene_id' => 'AP00G64240',
'e_value' => '3e-26',
'bit_score' => '120',
'alignment_length' => '373',
'identity_percentage' => '25.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'FBgn0260655' => array(
'gene_id' => 'FBgn0260655',
'e_value' => '1e-23',
'bit_score' => '112',
'alignment_length' => '617',
'identity_percentage' => '20.75',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_03G08000' => array(
'gene_id' => 'MRCC299_03G08000',
'e_value' => '9e-21',
'bit_score' => '103',
'alignment_length' => '831',
'identity_percentage' => '21.42',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_094G00020' => array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
[maximum depth reached]
)
),
'ENSMUSG00000033382' => array(
'gene_id' => 'ENSMUSG00000033382',
'e_value' => '4e-19',
'bit_score' => '98.2',
'alignment_length' => '438',
'identity_percentage' => '21.92',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
[maximum depth reached]
)
),
'ENSG00000153339' => array(
'gene_id' => 'ENSG00000153339',
'e_value' => '1e-18',
'bit_score' => '96.7',
'alignment_length' => '355',
'identity_percentage' => '22.82',
'species' => 'hom',
'common_name' => 'Homo sapiens',
'gf' => array(
[maximum depth reached]
)
),
'MP17G02120' => array(
'gene_id' => 'MP17G02120',
'e_value' => '2e-17',
'bit_score' => '92.4',
'alignment_length' => '418',
'identity_percentage' => '24.16',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'DDB_G0292682' => array(
'gene_id' => 'DDB_G0292682',
'e_value' => '1e-15',
'bit_score' => '87.0',
'alignment_length' => '637',
'identity_percentage' => '20.25',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
[maximum depth reached]
)
),
'PTI_21G02570' => array(
'gene_id' => 'PTI_21G02570',
'e_value' => '9e-15',
'bit_score' => '84.0',
'alignment_length' => '350',
'identity_percentage' => '24.29',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
[maximum depth reached]
)
),
'WBGene00018512' => array(
'gene_id' => 'WBGene00018512',
'e_value' => '2e-12',
'bit_score' => '75.9',
'alignment_length' => '487',
'identity_percentage' => '23.00',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
[maximum depth reached]
)
),
'phs344240' => array(
'gene_id' => 'phs344240',
'e_value' => '9e-12',
'bit_score' => '73.9',
'alignment_length' => '290',
'identity_percentage' => '23.10',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_094G00010' => array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
[maximum depth reached]
)
),
'Naga_100001g67' => array(
'gene_id' => 'Naga_100001g67',
'e_value' => '6e-10',
'bit_score' => '68.2',
'alignment_length' => '347',
'identity_percentage' => '24.78',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
[maximum depth reached]
)
),
'FC003G09000' => array(
'gene_id' => 'FC003G09000',
'e_value' => '4e-08',
'bit_score' => '62.0',
'alignment_length' => '360',
'identity_percentage' => '21.11',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
[maximum depth reached]
)
),
'emh741120' => array(
'gene_id' => 'emh741120',
'e_value' => '3e-07',
'bit_score' => '59.3',
'alignment_length' => '614',
'identity_percentage' => '20.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
[maximum depth reached]
)
),
'AA0024G00080' => array(
'gene_id' => 'AA0024G00080',
'e_value' => '1e-05',
'bit_score' => '54.3',
'alignment_length' => '117',
'identity_percentage' => '33.33',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'prcc4223' => array(
(int) 0 => 'RCC4223.05g02320'
),
'pse3' => array(
(int) 0 => 'PI00G14610'
),
'cvu' => array(
(int) 0 => 'CV00G05540'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_003G00300',
(int) 1 => 'CNC64A_003G00260'
),
'acg' => array(
(int) 0 => 'AC00G45200'
),
'ppa' => array(
(int) 0 => 'PP00270G00460'
),
'atr' => array(
(int) 0 => 'ATR_00030G00120'
),
'ath' => array(
(int) 0 => 'AT5G16280'
),
'osa' => array(
(int) 0 => 'OS03G57300'
),
'cre' => array(
(int) 0 => 'CR01G05390'
),
'vca' => array(
(int) 0 => 'VC00G45660'
),
'olu' => array(
(int) 0 => 'OL17G01190'
),
'ome' => array(
(int) 0 => 'OM_18G01010'
),
'ota' => array(
(int) 0 => 'OT_18G01170'
),
'orcc809' => array(
(int) 0 => 'ORCC809_17G01190'
),
'apr' => array(
(int) 0 => 'AP00G64240'
),
'drm' => array(
(int) 0 => 'FBgn0260655'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_03G08000'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000033382'
),
'hom' => array(
(int) 0 => 'ENSG00000153339'
),
'mpu' => array(
(int) 0 => 'MP17G02120'
),
'ddi' => array(
(int) 0 => 'DDB_G0292682'
),
'ptri' => array(
(int) 0 => 'PTI_21G02570'
),
'cel' => array(
(int) 0 => 'WBGene00018512'
),
'phs' => array(
(int) 0 => 'phs344240'
),
'nga' => array(
(int) 0 => 'Naga_100001g67'
),
'fcy' => array(
(int) 0 => 'FC003G09000'
),
'emh' => array(
(int) 0 => 'emh741120'
),
'aan' => array(
(int) 0 => 'AA0024G00080'
)
),
'gene_id' => 'RCC4223.05g02320',
'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' => 'RCC4223.05g02320',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'CM03G01680',
'gf_placeholder' => 'HOM03P014872',
'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(
'RCC4223.05g02320' => array(
'gene_id' => 'RCC4223.05g02320',
'e_value' => '0.0',
'bit_score' => '2335',
'alignment_length' => '1128',
'identity_percentage' => '100.00',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PI00G14610' => array(
'gene_id' => 'PI00G14610',
'e_value' => '0.0',
'bit_score' => '1986',
'alignment_length' => '1128',
'identity_percentage' => '84.93',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CV00G05540' => array(
'gene_id' => 'CV00G05540',
'e_value' => '4e-86',
'bit_score' => '309',
'alignment_length' => '1018',
'identity_percentage' => '26.72',
'species' => 'cvu',
'common_name' => 'Coccomyxa subellipsoidea C-169',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_003G00300' => array(
'gene_id' => 'CNC64A_003G00300',
'e_value' => '5e-70',
'bit_score' => '256',
'alignment_length' => '805',
'identity_percentage' => '27.58',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_003G00260' => array(
'gene_id' => 'CNC64A_003G00260',
'e_value' => '2e-69',
'bit_score' => '252',
'alignment_length' => '603',
'identity_percentage' => '30.18',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AC00G45200' => array(
'gene_id' => 'AC00G45200',
'e_value' => '8e-69',
'bit_score' => '253',
'alignment_length' => '954',
'identity_percentage' => '25.26',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PP00270G00460' => array(
'gene_id' => 'PP00270G00460',
'e_value' => '3e-53',
'bit_score' => '208',
'alignment_length' => '933',
'identity_percentage' => '24.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ATR_00030G00120' => array(
'gene_id' => 'ATR_00030G00120',
'e_value' => '4e-51',
'bit_score' => '201',
'alignment_length' => '842',
'identity_percentage' => '24.35',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AT5G16280' => array(
'gene_id' => 'AT5G16280',
'e_value' => '1e-49',
'bit_score' => '196',
'alignment_length' => '933',
'identity_percentage' => '23.26',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OS03G57300' => array(
'gene_id' => 'OS03G57300',
'e_value' => '1e-48',
'bit_score' => '193',
'alignment_length' => '748',
'identity_percentage' => '25.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CR01G05390' => array(
'gene_id' => 'CR01G05390',
'e_value' => '1e-45',
'bit_score' => '184',
'alignment_length' => '1110',
'identity_percentage' => '21.89',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'VC00G45660' => array(
'gene_id' => 'VC00G45660',
'e_value' => '2e-40',
'bit_score' => '167',
'alignment_length' => '1140',
'identity_percentage' => '21.84',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OL17G01190' => array(
'gene_id' => 'OL17G01190',
'e_value' => '3e-36',
'bit_score' => '153',
'alignment_length' => '646',
'identity_percentage' => '24.92',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OM_18G01010' => array(
'gene_id' => 'OM_18G01010',
'e_value' => '1e-33',
'bit_score' => '145',
'alignment_length' => '587',
'identity_percentage' => '23.68',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'OT_18G01170' => array(
'gene_id' => 'OT_18G01170',
'e_value' => '6e-29',
'bit_score' => '130',
'alignment_length' => '591',
'identity_percentage' => '23.18',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ORCC809_17G01190' => array(
'gene_id' => 'ORCC809_17G01190',
'e_value' => '6e-28',
'bit_score' => '126',
'alignment_length' => '902',
'identity_percentage' => '22.17',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'AP00G64240' => array(
'gene_id' => 'AP00G64240',
'e_value' => '3e-26',
'bit_score' => '120',
'alignment_length' => '373',
'identity_percentage' => '25.74',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'FBgn0260655' => array(
'gene_id' => 'FBgn0260655',
'e_value' => '1e-23',
'bit_score' => '112',
'alignment_length' => '617',
'identity_percentage' => '20.75',
'species' => 'drm',
'common_name' => 'Drosophila melanogaster',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'MRCC299_03G08000' => array(
'gene_id' => 'MRCC299_03G08000',
'e_value' => '9e-21',
'bit_score' => '103',
'alignment_length' => '831',
'identity_percentage' => '21.42',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_094G00020' => array(
'gene_id' => 'CNC64A_094G00020',
'e_value' => '3e-19',
'bit_score' => '94.4',
'alignment_length' => '158',
'identity_percentage' => '38.61',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ENSMUSG00000033382' => array(
'gene_id' => 'ENSMUSG00000033382',
'e_value' => '4e-19',
'bit_score' => '98.2',
'alignment_length' => '438',
'identity_percentage' => '21.92',
'species' => 'mus',
'common_name' => 'Mus musculus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'ENSG00000153339' => array(
'gene_id' => 'ENSG00000153339',
'e_value' => '1e-18',
'bit_score' => '96.7',
'alignment_length' => '355',
'identity_percentage' => '22.82',
'species' => 'hom',
'common_name' => 'Homo sapiens',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'MP17G02120' => array(
'gene_id' => 'MP17G02120',
'e_value' => '2e-17',
'bit_score' => '92.4',
'alignment_length' => '418',
'identity_percentage' => '24.16',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'DDB_G0292682' => array(
'gene_id' => 'DDB_G0292682',
'e_value' => '1e-15',
'bit_score' => '87.0',
'alignment_length' => '637',
'identity_percentage' => '20.25',
'species' => 'ddi',
'common_name' => 'Dictyostelium discoideum',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'PTI_21G02570' => array(
'gene_id' => 'PTI_21G02570',
'e_value' => '9e-15',
'bit_score' => '84.0',
'alignment_length' => '350',
'identity_percentage' => '24.29',
'species' => 'ptri',
'common_name' => 'Phaeodactylum tricornutum',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'WBGene00018512' => array(
'gene_id' => 'WBGene00018512',
'e_value' => '2e-12',
'bit_score' => '75.9',
'alignment_length' => '487',
'identity_percentage' => '23.00',
'species' => 'cel',
'common_name' => 'Caenorhabditis elegans',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'phs344240' => array(
'gene_id' => 'phs344240',
'e_value' => '9e-12',
'bit_score' => '73.9',
'alignment_length' => '290',
'identity_percentage' => '23.10',
'species' => 'phs',
'common_name' => 'Phytophtora sojae',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'CNC64A_094G00010' => array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
),
'Naga_100001g67' => array(
'gene_id' => 'Naga_100001g67',
'e_value' => '6e-10',
'bit_score' => '68.2',
'alignment_length' => '347',
'identity_percentage' => '24.78',
'species' => 'nga',
'common_name' => 'Nannochloropsis gaditana',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'FC003G09000' => array(
'gene_id' => 'FC003G09000',
'e_value' => '4e-08',
'bit_score' => '62.0',
'alignment_length' => '360',
'identity_percentage' => '21.11',
'species' => 'fcy',
'common_name' => 'Fragilariopsis cylindrus',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P038607'
)
),
'emh741120' => array(
'gene_id' => 'emh741120',
'e_value' => '3e-07',
'bit_score' => '59.3',
'alignment_length' => '614',
'identity_percentage' => '20.85',
'species' => 'emh',
'common_name' => 'Emiliania huxleyi',
'gf' => array(
'HOMFAM' => 'HOM03P008886',
'ORTHOFAM' => 'ORTHO03P009063'
)
),
'AA0024G00080' => array(
'gene_id' => 'AA0024G00080',
'e_value' => '1e-05',
'bit_score' => '54.3',
'alignment_length' => '117',
'identity_percentage' => '33.33',
'species' => 'aan',
'common_name' => 'Aureococcus anophagefferens',
'gf' => array(
'HOMFAM' => 'HOM03P034960',
'ORTHOFAM' => 'ORTHO03P034674'
)
)
)
$similarity_hits_species = array(
'prcc4223' => array(
(int) 0 => 'RCC4223.05g02320'
),
'pse3' => array(
(int) 0 => 'PI00G14610'
),
'cvu' => array(
(int) 0 => 'CV00G05540'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_003G00300',
(int) 1 => 'CNC64A_003G00260'
),
'acg' => array(
(int) 0 => 'AC00G45200'
),
'ppa' => array(
(int) 0 => 'PP00270G00460'
),
'atr' => array(
(int) 0 => 'ATR_00030G00120'
),
'ath' => array(
(int) 0 => 'AT5G16280'
),
'osa' => array(
(int) 0 => 'OS03G57300'
),
'cre' => array(
(int) 0 => 'CR01G05390'
),
'vca' => array(
(int) 0 => 'VC00G45660'
),
'olu' => array(
(int) 0 => 'OL17G01190'
),
'ome' => array(
(int) 0 => 'OM_18G01010'
),
'ota' => array(
(int) 0 => 'OT_18G01170'
),
'orcc809' => array(
(int) 0 => 'ORCC809_17G01190'
),
'apr' => array(
(int) 0 => 'AP00G64240'
),
'drm' => array(
(int) 0 => 'FBgn0260655'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_03G08000'
),
'mus' => array(
(int) 0 => 'ENSMUSG00000033382'
),
'hom' => array(
(int) 0 => 'ENSG00000153339'
),
'mpu' => array(
(int) 0 => 'MP17G02120'
),
'ddi' => array(
(int) 0 => 'DDB_G0292682'
),
'ptri' => array(
(int) 0 => 'PTI_21G02570'
),
'cel' => array(
(int) 0 => 'WBGene00018512'
),
'phs' => array(
(int) 0 => 'phs344240'
),
'nga' => array(
(int) 0 => 'Naga_100001g67'
),
'fcy' => array(
(int) 0 => 'FC003G09000'
),
'emh' => array(
(int) 0 => 'emh741120'
),
'aan' => array(
(int) 0 => 'AA0024G00080'
)
)
$gene_id = 'RCC4223.05g02320'
$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 = 'RCC4223.05g02320'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'CM03G01680'
$gf_placeholder = 'HOM03P014872'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_094G00010',
'e_value' => '2e-10',
'bit_score' => '65.9',
'alignment_length' => '122',
'identity_percentage' => '31.97',
'gf' => array(
'HOMFAM' => 'HOM03P002585',
'ORTHOFAM' => 'ORTHO03P002556'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_094G00010'
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-10 |
65.9 |
122 |
31.97 |