|
CNC64A_043G00190 |
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(
'AT1G11310' => array(
'gene_id' => 'AT1G11310',
'e_value' => '0.0',
'bit_score' => '1186',
'alignment_length' => '574',
'identity_percentage' => '100.00',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT1G61560' => array(
'gene_id' => 'AT1G61560',
'e_value' => '0.0',
'bit_score' => '897',
'alignment_length' => '592',
'identity_percentage' => '76.18',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT2G39200' => array(
'gene_id' => 'AT2G39200',
'e_value' => '0.0',
'bit_score' => '819',
'alignment_length' => '587',
'identity_percentage' => '68.31',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00034G00450' => array(
'gene_id' => 'ATR_00034G00450',
'e_value' => '0.0',
'bit_score' => '680',
'alignment_length' => '601',
'identity_percentage' => '57.07',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS03G03700' => array(
'gene_id' => 'OS03G03700',
'e_value' => '0.0',
'bit_score' => '529',
'alignment_length' => '521',
'identity_percentage' => '53.17',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G01050' => array(
'gene_id' => 'ATR_00044G01050',
'e_value' => '1e-176',
'bit_score' => '518',
'alignment_length' => '576',
'identity_percentage' => '49.48',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00108G00260' => array(
'gene_id' => 'ATR_00108G00260',
'e_value' => '5e-166',
'bit_score' => '491',
'alignment_length' => '508',
'identity_percentage' => '48.43',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS06G29110' => array(
'gene_id' => 'OS06G29110',
'e_value' => '3e-157',
'bit_score' => '468',
'alignment_length' => '508',
'identity_percentage' => '47.83',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'AT2G17480' => array(
'gene_id' => 'AT2G17480',
'e_value' => '4e-146',
'bit_score' => '441',
'alignment_length' => '571',
'identity_percentage' => '42.73',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT2G33670' => array(
'gene_id' => 'AT2G33670',
'e_value' => '4e-144',
'bit_score' => '433',
'alignment_length' => '480',
'identity_percentage' => '46.25',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT3G45290' => array(
'gene_id' => 'AT3G45290',
'e_value' => '1e-143',
'bit_score' => '432',
'alignment_length' => '487',
'identity_percentage' => '42.09',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT5G65970' => array(
'gene_id' => 'AT5G65970',
'e_value' => '4e-141',
'bit_score' => '428',
'alignment_length' => '540',
'identity_percentage' => '43.52',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT2G17430' => array(
'gene_id' => 'AT2G17430',
'e_value' => '1e-138',
'bit_score' => '421',
'alignment_length' => '470',
'identity_percentage' => '46.38',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT1G42560' => array(
'gene_id' => 'AT1G42560',
'e_value' => '5e-135',
'bit_score' => '408',
'alignment_length' => '461',
'identity_percentage' => '47.07',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'OS10G39520' => array(
'gene_id' => 'OS10G39520',
'e_value' => '1e-123',
'bit_score' => '380',
'alignment_length' => '420',
'identity_percentage' => '47.62',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00061G00090' => array(
'gene_id' => 'ATR_00061G00090',
'e_value' => '2e-120',
'bit_score' => '373',
'alignment_length' => '476',
'identity_percentage' => '42.65',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00066G00720' => array(
'gene_id' => 'ATR_00066G00720',
'e_value' => '3e-120',
'bit_score' => '372',
'alignment_length' => '518',
'identity_percentage' => '40.73',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS01G66510' => array(
'gene_id' => 'OS01G66510',
'e_value' => '1e-119',
'bit_score' => '370',
'alignment_length' => '483',
'identity_percentage' => '41.41',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'AT2G44110' => array(
'gene_id' => 'AT2G44110',
'e_value' => '2e-119',
'bit_score' => '369',
'alignment_length' => '484',
'identity_percentage' => '41.74',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT4G02600' => array(
'gene_id' => 'AT4G02600',
'e_value' => '3e-115',
'bit_score' => '360',
'alignment_length' => '491',
'identity_percentage' => '42.16',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT4G24250' => array(
'gene_id' => 'AT4G24250',
'e_value' => '3e-115',
'bit_score' => '358',
'alignment_length' => '490',
'identity_percentage' => '41.43',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00009G03790' => array(
'gene_id' => 'ATR_00009G03790',
'e_value' => '8e-108',
'bit_score' => '341',
'alignment_length' => '572',
'identity_percentage' => '36.89',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'PP00210G00390' => array(
'gene_id' => 'PP00210G00390',
'e_value' => '4e-105',
'bit_score' => '335',
'alignment_length' => '495',
'identity_percentage' => '38.18',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'AT1G26700' => array(
'gene_id' => 'AT1G26700',
'e_value' => '2e-103',
'bit_score' => '330',
'alignment_length' => '512',
'identity_percentage' => '38.09',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'OS04G36680' => array(
'gene_id' => 'OS04G36680',
'e_value' => '7e-100',
'bit_score' => '318',
'alignment_length' => '454',
'identity_percentage' => '42.51',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'AT5G53760' => array(
'gene_id' => 'AT5G53760',
'e_value' => '1e-99',
'bit_score' => '321',
'alignment_length' => '475',
'identity_percentage' => '37.47',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'PP00122G00590' => array(
'gene_id' => 'PP00122G00590',
'e_value' => '2e-99',
'bit_score' => '320',
'alignment_length' => '497',
'identity_percentage' => '38.63',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'PP00024G00070' => array(
'gene_id' => 'PP00024G00070',
'e_value' => '3e-97',
'bit_score' => '314',
'alignment_length' => '498',
'identity_percentage' => '38.55',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00070G00670' => array(
'gene_id' => 'ATR_00070G00670',
'e_value' => '6e-95',
'bit_score' => '308',
'alignment_length' => '473',
'identity_percentage' => '36.79',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G01020' => array(
'gene_id' => 'ATR_00044G01020',
'e_value' => '8e-95',
'bit_score' => '299',
'alignment_length' => '298',
'identity_percentage' => '55.03',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'PP00060G01010' => array(
'gene_id' => 'PP00060G01010',
'e_value' => '2e-94',
'bit_score' => '308',
'alignment_length' => '516',
'identity_percentage' => '35.66',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'OS05G09050' => array(
'gene_id' => 'OS05G09050',
'e_value' => '3e-94',
'bit_score' => '300',
'alignment_length' => '309',
'identity_percentage' => '47.25',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'PP00403G00240' => array(
'gene_id' => 'PP00403G00240',
'e_value' => '2e-93',
'bit_score' => '305',
'alignment_length' => '476',
'identity_percentage' => '36.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'PP00099G00630' => array(
'gene_id' => 'PP00099G00630',
'e_value' => '8e-93',
'bit_score' => '303',
'alignment_length' => '563',
'identity_percentage' => '38.01',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'OS11G07912' => array(
'gene_id' => 'OS11G07912',
'e_value' => '9e-93',
'bit_score' => '300',
'alignment_length' => '495',
'identity_percentage' => '34.55',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'PP00012G00320' => array(
'gene_id' => 'PP00012G00320',
'e_value' => '3e-90',
'bit_score' => '295',
'alignment_length' => '502',
'identity_percentage' => '35.46',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'PP00006G00500' => array(
'gene_id' => 'PP00006G00500',
'e_value' => '3e-88',
'bit_score' => '293',
'alignment_length' => '554',
'identity_percentage' => '32.67',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'OS02G10350' => array(
'gene_id' => 'OS02G10350',
'e_value' => '1e-87',
'bit_score' => '286',
'alignment_length' => '475',
'identity_percentage' => '38.32',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'PP00296G00240' => array(
'gene_id' => 'PP00296G00240',
'e_value' => '3e-84',
'bit_score' => '279',
'alignment_length' => '483',
'identity_percentage' => '38.51',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'AT1G11000' => array(
'gene_id' => 'AT1G11000',
'e_value' => '4e-84',
'bit_score' => '280',
'alignment_length' => '477',
'identity_percentage' => '35.85',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'PP00060G00990' => array(
'gene_id' => 'PP00060G00990',
'e_value' => '4e-76',
'bit_score' => '260',
'alignment_length' => '486',
'identity_percentage' => '34.36',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'PP00060G00970' => array(
'gene_id' => 'PP00060G00970',
'e_value' => '3e-66',
'bit_score' => '230',
'alignment_length' => '454',
'identity_percentage' => '35.46',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G00940' => array(
'gene_id' => 'ATR_00044G00940',
'e_value' => '9e-56',
'bit_score' => '194',
'alignment_length' => '213',
'identity_percentage' => '46.48',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS05G34550' => array(
'gene_id' => 'OS05G34550',
'e_value' => '8e-55',
'bit_score' => '194',
'alignment_length' => '291',
'identity_percentage' => '41.92',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'OS04G58420' => array(
'gene_id' => 'OS04G58420',
'e_value' => '6e-39',
'bit_score' => '150',
'alignment_length' => '176',
'identity_percentage' => '40.91',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'OS02G35490' => array(
'gene_id' => 'OS02G35490',
'e_value' => '2e-35',
'bit_score' => '136',
'alignment_length' => '195',
'identity_percentage' => '42.05',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'OS06G40790' => array(
'gene_id' => 'OS06G40790',
'e_value' => '8e-32',
'bit_score' => '131',
'alignment_length' => '226',
'identity_percentage' => '35.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G01030' => array(
'gene_id' => 'ATR_00044G01030',
'e_value' => '5e-31',
'bit_score' => '125',
'alignment_length' => '237',
'identity_percentage' => '34.60',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OT_13G00440' => array(
'gene_id' => 'OT_13G00440',
'e_value' => '1e-27',
'bit_score' => '122',
'alignment_length' => '471',
'identity_percentage' => '25.05',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'OM_08G04030' => array(
'gene_id' => 'OM_08G04030',
'e_value' => '3e-25',
'bit_score' => '114',
'alignment_length' => '456',
'identity_percentage' => '26.10',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'BPRRCC1105_02G06140' => array(
'gene_id' => 'BPRRCC1105_02G06140',
'e_value' => '3e-23',
'bit_score' => '108',
'alignment_length' => '334',
'identity_percentage' => '27.54',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
[maximum depth reached]
)
),
'OL13G00410' => array(
'gene_id' => 'OL13G00410',
'e_value' => '9e-22',
'bit_score' => '103',
'alignment_length' => '328',
'identity_percentage' => '28.35',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_13G02620' => array(
'gene_id' => 'ORCC809_13G02620',
'e_value' => '1e-21',
'bit_score' => '103',
'alignment_length' => '328',
'identity_percentage' => '26.83',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_009G01200' => array(
'gene_id' => 'CNC64A_009G01200',
'e_value' => '3e-17',
'bit_score' => '89.0',
'alignment_length' => '429',
'identity_percentage' => '25.64',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G00930' => array(
'gene_id' => 'ATR_00044G00930',
'e_value' => '5e-17',
'bit_score' => '81.3',
'alignment_length' => '57',
'identity_percentage' => '68.42',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.11g01460' => array(
'gene_id' => 'RCC4223.11g01460',
'e_value' => '6e-17',
'bit_score' => '88.2',
'alignment_length' => '266',
'identity_percentage' => '28.95',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G12690' => array(
'gene_id' => 'PI00G12690',
'e_value' => '4e-16',
'bit_score' => '85.5',
'alignment_length' => '231',
'identity_percentage' => '29.87',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'VC00G46120' => array(
'gene_id' => 'VC00G46120',
'e_value' => '4e-15',
'bit_score' => '82.8',
'alignment_length' => '353',
'identity_percentage' => '24.36',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'PI00G23890' => array(
'gene_id' => 'PI00G23890',
'e_value' => '3e-14',
'bit_score' => '79.7',
'alignment_length' => '207',
'identity_percentage' => '28.02',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_07G01620' => array(
'gene_id' => 'MRCC299_07G01620',
'e_value' => '8e-14',
'bit_score' => '78.2',
'alignment_length' => '196',
'identity_percentage' => '30.10',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.03g08940' => array(
'gene_id' => 'RCC4223.03g08940',
'e_value' => '1e-13',
'bit_score' => '77.8',
'alignment_length' => '226',
'identity_percentage' => '28.32',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'AC00G50730' => array(
'gene_id' => 'AC00G50730',
'e_value' => '1e-11',
'bit_score' => '71.2',
'alignment_length' => '250',
'identity_percentage' => '26.80',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'AP00G43030' => array(
'gene_id' => 'AP00G43030',
'e_value' => '2e-10',
'bit_score' => '68.2',
'alignment_length' => '212',
'identity_percentage' => '29.25',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'AP00G35900' => array(
'gene_id' => 'AP00G35900',
'e_value' => '2e-09',
'bit_score' => '64.7',
'alignment_length' => '214',
'identity_percentage' => '28.50',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'CR01G03670' => array(
'gene_id' => 'CR01G03670',
'e_value' => '4e-09',
'bit_score' => '63.9',
'alignment_length' => '186',
'identity_percentage' => '24.73',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'VC00G12520' => array(
'gene_id' => 'VC00G12520',
'e_value' => '6e-09',
'bit_score' => '63.5',
'alignment_length' => '327',
'identity_percentage' => '25.38',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_043G00190' => array(
'gene_id' => 'CNC64A_043G00190',
'e_value' => '2e-07',
'bit_score' => '57.8',
'alignment_length' => '242',
'identity_percentage' => '23.97',
'gf' => array(
[maximum depth reached]
)
),
'MP01G06640' => array(
'gene_id' => 'MP01G06640',
'e_value' => '6e-07',
'bit_score' => '56.2',
'alignment_length' => '182',
'identity_percentage' => '26.92',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'AC00G50740' => array(
'gene_id' => 'AC00G50740',
'e_value' => '4e-06',
'bit_score' => '50.4',
'alignment_length' => '86',
'identity_percentage' => '32.56',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'ath' => array(
(int) 0 => 'AT1G11310',
(int) 1 => 'AT1G61560',
(int) 2 => 'AT2G39200',
(int) 3 => 'AT2G17480',
(int) 4 => 'AT2G33670',
(int) 5 => 'AT3G45290',
(int) 6 => 'AT5G65970',
(int) 7 => 'AT2G17430',
(int) 8 => 'AT1G42560',
(int) 9 => 'AT2G44110',
(int) 10 => 'AT4G02600',
(int) 11 => 'AT4G24250',
(int) 12 => 'AT1G26700',
(int) 13 => 'AT5G53760',
(int) 14 => 'AT1G11000'
),
'atr' => array(
(int) 0 => 'ATR_00034G00450',
(int) 1 => 'ATR_00044G01050',
(int) 2 => 'ATR_00108G00260',
(int) 3 => 'ATR_00061G00090',
(int) 4 => 'ATR_00066G00720',
(int) 5 => 'ATR_00009G03790',
(int) 6 => 'ATR_00070G00670',
(int) 7 => 'ATR_00044G01020',
(int) 8 => 'ATR_00044G00940',
(int) 9 => 'ATR_00044G01030',
(int) 10 => 'ATR_00044G00930'
),
'osa' => array(
(int) 0 => 'OS03G03700',
(int) 1 => 'OS06G29110',
(int) 2 => 'OS10G39520',
(int) 3 => 'OS01G66510',
(int) 4 => 'OS04G36680',
(int) 5 => 'OS05G09050',
(int) 6 => 'OS11G07912',
(int) 7 => 'OS02G10350',
(int) 8 => 'OS05G34550',
(int) 9 => 'OS04G58420',
(int) 10 => 'OS02G35490',
(int) 11 => 'OS06G40790'
),
'ppa' => array(
(int) 0 => 'PP00210G00390',
(int) 1 => 'PP00122G00590',
(int) 2 => 'PP00024G00070',
(int) 3 => 'PP00060G01010',
(int) 4 => 'PP00403G00240',
(int) 5 => 'PP00099G00630',
(int) 6 => 'PP00012G00320',
(int) 7 => 'PP00006G00500',
(int) 8 => 'PP00296G00240',
(int) 9 => 'PP00060G00990',
(int) 10 => 'PP00060G00970'
),
'ota' => array(
(int) 0 => 'OT_13G00440'
),
'ome' => array(
(int) 0 => 'OM_08G04030'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_02G06140'
),
'olu' => array(
(int) 0 => 'OL13G00410'
),
'orcc809' => array(
(int) 0 => 'ORCC809_13G02620'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_009G01200'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.11g01460',
(int) 1 => 'RCC4223.03g08940'
),
'pse3' => array(
(int) 0 => 'PI00G12690',
(int) 1 => 'PI00G23890'
),
'vca' => array(
(int) 0 => 'VC00G46120',
(int) 1 => 'VC00G12520'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_07G01620'
),
'acg' => array(
(int) 0 => 'AC00G50730',
(int) 1 => 'AC00G50740'
),
'apr' => array(
(int) 0 => 'AP00G43030',
(int) 1 => 'AP00G35900'
),
'cre' => array(
(int) 0 => 'CR01G03670'
),
'mpu' => array(
(int) 0 => 'MP01G06640'
)
),
'gene_id' => 'AT1G11310',
'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' => 'AT1G11310',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'WBGene00021049',
'gf_placeholder' => 'HOM03P008896',
'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(
'AT1G11310' => array(
'gene_id' => 'AT1G11310',
'e_value' => '0.0',
'bit_score' => '1186',
'alignment_length' => '574',
'identity_percentage' => '100.00',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT1G61560' => array(
'gene_id' => 'AT1G61560',
'e_value' => '0.0',
'bit_score' => '897',
'alignment_length' => '592',
'identity_percentage' => '76.18',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT2G39200' => array(
'gene_id' => 'AT2G39200',
'e_value' => '0.0',
'bit_score' => '819',
'alignment_length' => '587',
'identity_percentage' => '68.31',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'ATR_00034G00450' => array(
'gene_id' => 'ATR_00034G00450',
'e_value' => '0.0',
'bit_score' => '680',
'alignment_length' => '601',
'identity_percentage' => '57.07',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'OS03G03700' => array(
'gene_id' => 'OS03G03700',
'e_value' => '0.0',
'bit_score' => '529',
'alignment_length' => '521',
'identity_percentage' => '53.17',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'ATR_00044G01050' => array(
'gene_id' => 'ATR_00044G01050',
'e_value' => '1e-176',
'bit_score' => '518',
'alignment_length' => '576',
'identity_percentage' => '49.48',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'ATR_00108G00260' => array(
'gene_id' => 'ATR_00108G00260',
'e_value' => '5e-166',
'bit_score' => '491',
'alignment_length' => '508',
'identity_percentage' => '48.43',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P156863'
)
),
'OS06G29110' => array(
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'e_value' => '3e-157',
'bit_score' => '468',
'alignment_length' => '508',
'identity_percentage' => '47.83',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT2G17480' => array(
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'e_value' => '4e-146',
'bit_score' => '441',
'alignment_length' => '571',
'identity_percentage' => '42.73',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT2G33670' => array(
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'e_value' => '4e-144',
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'alignment_length' => '480',
'identity_percentage' => '46.25',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT3G45290' => array(
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'e_value' => '1e-143',
'bit_score' => '432',
'alignment_length' => '487',
'identity_percentage' => '42.09',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P148497'
)
),
'AT5G65970' => array(
'gene_id' => 'AT5G65970',
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'bit_score' => '428',
'alignment_length' => '540',
'identity_percentage' => '43.52',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT2G17430' => array(
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'e_value' => '1e-138',
'bit_score' => '421',
'alignment_length' => '470',
'identity_percentage' => '46.38',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT1G42560' => array(
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'e_value' => '5e-135',
'bit_score' => '408',
'alignment_length' => '461',
'identity_percentage' => '47.07',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'OS10G39520' => array(
'gene_id' => 'OS10G39520',
'e_value' => '1e-123',
'bit_score' => '380',
'alignment_length' => '420',
'identity_percentage' => '47.62',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'ATR_00061G00090' => array(
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'e_value' => '2e-120',
'bit_score' => '373',
'alignment_length' => '476',
'identity_percentage' => '42.65',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'ATR_00066G00720' => array(
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'e_value' => '3e-120',
'bit_score' => '372',
'alignment_length' => '518',
'identity_percentage' => '40.73',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'OS01G66510' => array(
'gene_id' => 'OS01G66510',
'e_value' => '1e-119',
'bit_score' => '370',
'alignment_length' => '483',
'identity_percentage' => '41.41',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'AT2G44110' => array(
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'e_value' => '2e-119',
'bit_score' => '369',
'alignment_length' => '484',
'identity_percentage' => '41.74',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'AT4G02600' => array(
'gene_id' => 'AT4G02600',
'e_value' => '3e-115',
'bit_score' => '360',
'alignment_length' => '491',
'identity_percentage' => '42.16',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'AT4G24250' => array(
'gene_id' => 'AT4G24250',
'e_value' => '3e-115',
'bit_score' => '358',
'alignment_length' => '490',
'identity_percentage' => '41.43',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'ATR_00009G03790' => array(
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'e_value' => '8e-108',
'bit_score' => '341',
'alignment_length' => '572',
'identity_percentage' => '36.89',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'PP00210G00390' => array(
'gene_id' => 'PP00210G00390',
'e_value' => '4e-105',
'bit_score' => '335',
'alignment_length' => '495',
'identity_percentage' => '38.18',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'AT1G26700' => array(
'gene_id' => 'AT1G26700',
'e_value' => '2e-103',
'bit_score' => '330',
'alignment_length' => '512',
'identity_percentage' => '38.09',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'OS04G36680' => array(
'gene_id' => 'OS04G36680',
'e_value' => '7e-100',
'bit_score' => '318',
'alignment_length' => '454',
'identity_percentage' => '42.51',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P169369'
)
),
'AT5G53760' => array(
'gene_id' => 'AT5G53760',
'e_value' => '1e-99',
'bit_score' => '321',
'alignment_length' => '475',
'identity_percentage' => '37.47',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'PP00122G00590' => array(
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'e_value' => '2e-99',
'bit_score' => '320',
'alignment_length' => '497',
'identity_percentage' => '38.63',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'PP00024G00070' => array(
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'e_value' => '3e-97',
'bit_score' => '314',
'alignment_length' => '498',
'identity_percentage' => '38.55',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'ATR_00070G00670' => array(
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'e_value' => '6e-95',
'bit_score' => '308',
'alignment_length' => '473',
'identity_percentage' => '36.79',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P038392'
)
),
'ATR_00044G01020' => array(
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'e_value' => '8e-95',
'bit_score' => '299',
'alignment_length' => '298',
'identity_percentage' => '55.03',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P194291'
)
),
'PP00060G01010' => array(
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'e_value' => '2e-94',
'bit_score' => '308',
'alignment_length' => '516',
'identity_percentage' => '35.66',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'OS05G09050' => array(
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'e_value' => '3e-94',
'bit_score' => '300',
'alignment_length' => '309',
'identity_percentage' => '47.25',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'PP00403G00240' => array(
'gene_id' => 'PP00403G00240',
'e_value' => '2e-93',
'bit_score' => '305',
'alignment_length' => '476',
'identity_percentage' => '36.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'PP00099G00630' => array(
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'e_value' => '8e-93',
'bit_score' => '303',
'alignment_length' => '563',
'identity_percentage' => '38.01',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'OS11G07912' => array(
'gene_id' => 'OS11G07912',
'e_value' => '9e-93',
'bit_score' => '300',
'alignment_length' => '495',
'identity_percentage' => '34.55',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P038392'
)
),
'PP00012G00320' => array(
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'e_value' => '3e-90',
'bit_score' => '295',
'alignment_length' => '502',
'identity_percentage' => '35.46',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'PP00006G00500' => array(
'gene_id' => 'PP00006G00500',
'e_value' => '3e-88',
'bit_score' => '293',
'alignment_length' => '554',
'identity_percentage' => '32.67',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'OS02G10350' => array(
'gene_id' => 'OS02G10350',
'e_value' => '1e-87',
'bit_score' => '286',
'alignment_length' => '475',
'identity_percentage' => '38.32',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P122700'
)
),
'PP00296G00240' => array(
'gene_id' => 'PP00296G00240',
'e_value' => '3e-84',
'bit_score' => '279',
'alignment_length' => '483',
'identity_percentage' => '38.51',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'AT1G11000' => array(
'gene_id' => 'AT1G11000',
'e_value' => '4e-84',
'bit_score' => '280',
'alignment_length' => '477',
'identity_percentage' => '35.85',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P038392'
)
),
'PP00060G00990' => array(
'gene_id' => 'PP00060G00990',
'e_value' => '4e-76',
'bit_score' => '260',
'alignment_length' => '486',
'identity_percentage' => '34.36',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'PP00060G00970' => array(
'gene_id' => 'PP00060G00970',
'e_value' => '3e-66',
'bit_score' => '230',
'alignment_length' => '454',
'identity_percentage' => '35.46',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P191922'
)
),
'ATR_00044G00940' => array(
'gene_id' => 'ATR_00044G00940',
'e_value' => '9e-56',
'bit_score' => '194',
'alignment_length' => '213',
'identity_percentage' => '46.48',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P186901'
)
),
'OS05G34550' => array(
'gene_id' => 'OS05G34550',
'e_value' => '8e-55',
'bit_score' => '194',
'alignment_length' => '291',
'identity_percentage' => '41.92',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P038706'
)
),
'OS04G58420' => array(
'gene_id' => 'OS04G58420',
'e_value' => '6e-39',
'bit_score' => '150',
'alignment_length' => '176',
'identity_percentage' => '40.91',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P135994'
)
),
'OS02G35490' => array(
'gene_id' => 'OS02G35490',
'e_value' => '2e-35',
'bit_score' => '136',
'alignment_length' => '195',
'identity_percentage' => '42.05',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P115802'
)
),
'OS06G40790' => array(
'gene_id' => 'OS06G40790',
'e_value' => '8e-32',
'bit_score' => '131',
'alignment_length' => '226',
'identity_percentage' => '35.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P181184'
)
),
'ATR_00044G01030' => array(
'gene_id' => 'ATR_00044G01030',
'e_value' => '5e-31',
'bit_score' => '125',
'alignment_length' => '237',
'identity_percentage' => '34.60',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P080727'
)
),
'OT_13G00440' => array(
'gene_id' => 'OT_13G00440',
'e_value' => '1e-27',
'bit_score' => '122',
'alignment_length' => '471',
'identity_percentage' => '25.05',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'OM_08G04030' => array(
'gene_id' => 'OM_08G04030',
'e_value' => '3e-25',
'bit_score' => '114',
'alignment_length' => '456',
'identity_percentage' => '26.10',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'BPRRCC1105_02G06140' => array(
'gene_id' => 'BPRRCC1105_02G06140',
'e_value' => '3e-23',
'bit_score' => '108',
'alignment_length' => '334',
'identity_percentage' => '27.54',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'OL13G00410' => array(
'gene_id' => 'OL13G00410',
'e_value' => '9e-22',
'bit_score' => '103',
'alignment_length' => '328',
'identity_percentage' => '28.35',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'ORCC809_13G02620' => array(
'gene_id' => 'ORCC809_13G02620',
'e_value' => '1e-21',
'bit_score' => '103',
'alignment_length' => '328',
'identity_percentage' => '26.83',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'CNC64A_009G01200' => array(
'gene_id' => 'CNC64A_009G01200',
'e_value' => '3e-17',
'bit_score' => '89.0',
'alignment_length' => '429',
'identity_percentage' => '25.64',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'ATR_00044G00930' => array(
'gene_id' => 'ATR_00044G00930',
'e_value' => '5e-17',
'bit_score' => '81.3',
'alignment_length' => '57',
'identity_percentage' => '68.42',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P099355'
)
),
'RCC4223.11g01460' => array(
'gene_id' => 'RCC4223.11g01460',
'e_value' => '6e-17',
'bit_score' => '88.2',
'alignment_length' => '266',
'identity_percentage' => '28.95',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'PI00G12690' => array(
'gene_id' => 'PI00G12690',
'e_value' => '4e-16',
'bit_score' => '85.5',
'alignment_length' => '231',
'identity_percentage' => '29.87',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'VC00G46120' => array(
'gene_id' => 'VC00G46120',
'e_value' => '4e-15',
'bit_score' => '82.8',
'alignment_length' => '353',
'identity_percentage' => '24.36',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'PI00G23890' => array(
'gene_id' => 'PI00G23890',
'e_value' => '3e-14',
'bit_score' => '79.7',
'alignment_length' => '207',
'identity_percentage' => '28.02',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'MRCC299_07G01620' => array(
'gene_id' => 'MRCC299_07G01620',
'e_value' => '8e-14',
'bit_score' => '78.2',
'alignment_length' => '196',
'identity_percentage' => '30.10',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P064501'
)
),
'RCC4223.03g08940' => array(
'gene_id' => 'RCC4223.03g08940',
'e_value' => '1e-13',
'bit_score' => '77.8',
'alignment_length' => '226',
'identity_percentage' => '28.32',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'AC00G50730' => array(
'gene_id' => 'AC00G50730',
'e_value' => '1e-11',
'bit_score' => '71.2',
'alignment_length' => '250',
'identity_percentage' => '26.80',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P131296'
)
),
'AP00G43030' => array(
'gene_id' => 'AP00G43030',
'e_value' => '2e-10',
'bit_score' => '68.2',
'alignment_length' => '212',
'identity_percentage' => '29.25',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'AP00G35900' => array(
'gene_id' => 'AP00G35900',
'e_value' => '2e-09',
'bit_score' => '64.7',
'alignment_length' => '214',
'identity_percentage' => '28.50',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P067884'
)
),
'CR01G03670' => array(
'gene_id' => 'CR01G03670',
'e_value' => '4e-09',
'bit_score' => '63.9',
'alignment_length' => '186',
'identity_percentage' => '24.73',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P196749'
)
),
'VC00G12520' => array(
'gene_id' => 'VC00G12520',
'e_value' => '6e-09',
'bit_score' => '63.5',
'alignment_length' => '327',
'identity_percentage' => '25.38',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P191262'
)
),
'CNC64A_043G00190' => array(
'gene_id' => 'CNC64A_043G00190',
'e_value' => '2e-07',
'bit_score' => '57.8',
'alignment_length' => '242',
'identity_percentage' => '23.97',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'MP01G06640' => array(
'gene_id' => 'MP01G06640',
'e_value' => '6e-07',
'bit_score' => '56.2',
'alignment_length' => '182',
'identity_percentage' => '26.92',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P064501'
)
),
'AC00G50740' => array(
'gene_id' => 'AC00G50740',
'e_value' => '4e-06',
'bit_score' => '50.4',
'alignment_length' => '86',
'identity_percentage' => '32.56',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P038706'
)
)
)
$similarity_hits_species = array(
'ath' => array(
(int) 0 => 'AT1G11310',
(int) 1 => 'AT1G61560',
(int) 2 => 'AT2G39200',
(int) 3 => 'AT2G17480',
(int) 4 => 'AT2G33670',
(int) 5 => 'AT3G45290',
(int) 6 => 'AT5G65970',
(int) 7 => 'AT2G17430',
(int) 8 => 'AT1G42560',
(int) 9 => 'AT2G44110',
(int) 10 => 'AT4G02600',
(int) 11 => 'AT4G24250',
(int) 12 => 'AT1G26700',
(int) 13 => 'AT5G53760',
(int) 14 => 'AT1G11000'
),
'atr' => array(
(int) 0 => 'ATR_00034G00450',
(int) 1 => 'ATR_00044G01050',
(int) 2 => 'ATR_00108G00260',
(int) 3 => 'ATR_00061G00090',
(int) 4 => 'ATR_00066G00720',
(int) 5 => 'ATR_00009G03790',
(int) 6 => 'ATR_00070G00670',
(int) 7 => 'ATR_00044G01020',
(int) 8 => 'ATR_00044G00940',
(int) 9 => 'ATR_00044G01030',
(int) 10 => 'ATR_00044G00930'
),
'osa' => array(
(int) 0 => 'OS03G03700',
(int) 1 => 'OS06G29110',
(int) 2 => 'OS10G39520',
(int) 3 => 'OS01G66510',
(int) 4 => 'OS04G36680',
(int) 5 => 'OS05G09050',
(int) 6 => 'OS11G07912',
(int) 7 => 'OS02G10350',
(int) 8 => 'OS05G34550',
(int) 9 => 'OS04G58420',
(int) 10 => 'OS02G35490',
(int) 11 => 'OS06G40790'
),
'ppa' => array(
(int) 0 => 'PP00210G00390',
(int) 1 => 'PP00122G00590',
(int) 2 => 'PP00024G00070',
(int) 3 => 'PP00060G01010',
(int) 4 => 'PP00403G00240',
(int) 5 => 'PP00099G00630',
(int) 6 => 'PP00012G00320',
(int) 7 => 'PP00006G00500',
(int) 8 => 'PP00296G00240',
(int) 9 => 'PP00060G00990',
(int) 10 => 'PP00060G00970'
),
'ota' => array(
(int) 0 => 'OT_13G00440'
),
'ome' => array(
(int) 0 => 'OM_08G04030'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_02G06140'
),
'olu' => array(
(int) 0 => 'OL13G00410'
),
'orcc809' => array(
(int) 0 => 'ORCC809_13G02620'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_009G01200'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.11g01460',
(int) 1 => 'RCC4223.03g08940'
),
'pse3' => array(
(int) 0 => 'PI00G12690',
(int) 1 => 'PI00G23890'
),
'vca' => array(
(int) 0 => 'VC00G46120',
(int) 1 => 'VC00G12520'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_07G01620'
),
'acg' => array(
(int) 0 => 'AC00G50730',
(int) 1 => 'AC00G50740'
),
'apr' => array(
(int) 0 => 'AP00G43030',
(int) 1 => 'AP00G35900'
),
'cre' => array(
(int) 0 => 'CR01G03670'
),
'mpu' => array(
(int) 0 => 'MP01G06640'
)
)
$gene_id = 'AT1G11310'
$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 = 'AT1G11310'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'WBGene00021049'
$gf_placeholder = 'HOM03P008896'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_043G00190',
'e_value' => '2e-07',
'bit_score' => '57.8',
'alignment_length' => '242',
'identity_percentage' => '23.97',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_043G00190'
include - APP/View/Analysis/custom_tree_creation.ctp, line 169
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 146
Notice (8): Undefined index: common_name [APP/View/Analysis/custom_tree_creation.ctp, line 169]Code Context echo "<td><input type='checkbox' name='selected_genes[]' value='".$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(
'AT1G11310' => array(
'gene_id' => 'AT1G11310',
'e_value' => '0.0',
'bit_score' => '1186',
'alignment_length' => '574',
'identity_percentage' => '100.00',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT1G61560' => array(
'gene_id' => 'AT1G61560',
'e_value' => '0.0',
'bit_score' => '897',
'alignment_length' => '592',
'identity_percentage' => '76.18',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT2G39200' => array(
'gene_id' => 'AT2G39200',
'e_value' => '0.0',
'bit_score' => '819',
'alignment_length' => '587',
'identity_percentage' => '68.31',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00034G00450' => array(
'gene_id' => 'ATR_00034G00450',
'e_value' => '0.0',
'bit_score' => '680',
'alignment_length' => '601',
'identity_percentage' => '57.07',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS03G03700' => array(
'gene_id' => 'OS03G03700',
'e_value' => '0.0',
'bit_score' => '529',
'alignment_length' => '521',
'identity_percentage' => '53.17',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G01050' => array(
'gene_id' => 'ATR_00044G01050',
'e_value' => '1e-176',
'bit_score' => '518',
'alignment_length' => '576',
'identity_percentage' => '49.48',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00108G00260' => array(
'gene_id' => 'ATR_00108G00260',
'e_value' => '5e-166',
'bit_score' => '491',
'alignment_length' => '508',
'identity_percentage' => '48.43',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS06G29110' => array(
'gene_id' => 'OS06G29110',
'e_value' => '3e-157',
'bit_score' => '468',
'alignment_length' => '508',
'identity_percentage' => '47.83',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'AT2G17480' => array(
'gene_id' => 'AT2G17480',
'e_value' => '4e-146',
'bit_score' => '441',
'alignment_length' => '571',
'identity_percentage' => '42.73',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT2G33670' => array(
'gene_id' => 'AT2G33670',
'e_value' => '4e-144',
'bit_score' => '433',
'alignment_length' => '480',
'identity_percentage' => '46.25',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT3G45290' => array(
'gene_id' => 'AT3G45290',
'e_value' => '1e-143',
'bit_score' => '432',
'alignment_length' => '487',
'identity_percentage' => '42.09',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT5G65970' => array(
'gene_id' => 'AT5G65970',
'e_value' => '4e-141',
'bit_score' => '428',
'alignment_length' => '540',
'identity_percentage' => '43.52',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT2G17430' => array(
'gene_id' => 'AT2G17430',
'e_value' => '1e-138',
'bit_score' => '421',
'alignment_length' => '470',
'identity_percentage' => '46.38',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT1G42560' => array(
'gene_id' => 'AT1G42560',
'e_value' => '5e-135',
'bit_score' => '408',
'alignment_length' => '461',
'identity_percentage' => '47.07',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'OS10G39520' => array(
'gene_id' => 'OS10G39520',
'e_value' => '1e-123',
'bit_score' => '380',
'alignment_length' => '420',
'identity_percentage' => '47.62',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00061G00090' => array(
'gene_id' => 'ATR_00061G00090',
'e_value' => '2e-120',
'bit_score' => '373',
'alignment_length' => '476',
'identity_percentage' => '42.65',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00066G00720' => array(
'gene_id' => 'ATR_00066G00720',
'e_value' => '3e-120',
'bit_score' => '372',
'alignment_length' => '518',
'identity_percentage' => '40.73',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS01G66510' => array(
'gene_id' => 'OS01G66510',
'e_value' => '1e-119',
'bit_score' => '370',
'alignment_length' => '483',
'identity_percentage' => '41.41',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'AT2G44110' => array(
'gene_id' => 'AT2G44110',
'e_value' => '2e-119',
'bit_score' => '369',
'alignment_length' => '484',
'identity_percentage' => '41.74',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT4G02600' => array(
'gene_id' => 'AT4G02600',
'e_value' => '3e-115',
'bit_score' => '360',
'alignment_length' => '491',
'identity_percentage' => '42.16',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'AT4G24250' => array(
'gene_id' => 'AT4G24250',
'e_value' => '3e-115',
'bit_score' => '358',
'alignment_length' => '490',
'identity_percentage' => '41.43',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00009G03790' => array(
'gene_id' => 'ATR_00009G03790',
'e_value' => '8e-108',
'bit_score' => '341',
'alignment_length' => '572',
'identity_percentage' => '36.89',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'PP00210G00390' => array(
'gene_id' => 'PP00210G00390',
'e_value' => '4e-105',
'bit_score' => '335',
'alignment_length' => '495',
'identity_percentage' => '38.18',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'AT1G26700' => array(
'gene_id' => 'AT1G26700',
'e_value' => '2e-103',
'bit_score' => '330',
'alignment_length' => '512',
'identity_percentage' => '38.09',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'OS04G36680' => array(
'gene_id' => 'OS04G36680',
'e_value' => '7e-100',
'bit_score' => '318',
'alignment_length' => '454',
'identity_percentage' => '42.51',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'AT5G53760' => array(
'gene_id' => 'AT5G53760',
'e_value' => '1e-99',
'bit_score' => '321',
'alignment_length' => '475',
'identity_percentage' => '37.47',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'PP00122G00590' => array(
'gene_id' => 'PP00122G00590',
'e_value' => '2e-99',
'bit_score' => '320',
'alignment_length' => '497',
'identity_percentage' => '38.63',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'PP00024G00070' => array(
'gene_id' => 'PP00024G00070',
'e_value' => '3e-97',
'bit_score' => '314',
'alignment_length' => '498',
'identity_percentage' => '38.55',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00070G00670' => array(
'gene_id' => 'ATR_00070G00670',
'e_value' => '6e-95',
'bit_score' => '308',
'alignment_length' => '473',
'identity_percentage' => '36.79',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G01020' => array(
'gene_id' => 'ATR_00044G01020',
'e_value' => '8e-95',
'bit_score' => '299',
'alignment_length' => '298',
'identity_percentage' => '55.03',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'PP00060G01010' => array(
'gene_id' => 'PP00060G01010',
'e_value' => '2e-94',
'bit_score' => '308',
'alignment_length' => '516',
'identity_percentage' => '35.66',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'OS05G09050' => array(
'gene_id' => 'OS05G09050',
'e_value' => '3e-94',
'bit_score' => '300',
'alignment_length' => '309',
'identity_percentage' => '47.25',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'PP00403G00240' => array(
'gene_id' => 'PP00403G00240',
'e_value' => '2e-93',
'bit_score' => '305',
'alignment_length' => '476',
'identity_percentage' => '36.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'PP00099G00630' => array(
'gene_id' => 'PP00099G00630',
'e_value' => '8e-93',
'bit_score' => '303',
'alignment_length' => '563',
'identity_percentage' => '38.01',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'OS11G07912' => array(
'gene_id' => 'OS11G07912',
'e_value' => '9e-93',
'bit_score' => '300',
'alignment_length' => '495',
'identity_percentage' => '34.55',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'PP00012G00320' => array(
'gene_id' => 'PP00012G00320',
'e_value' => '3e-90',
'bit_score' => '295',
'alignment_length' => '502',
'identity_percentage' => '35.46',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'PP00006G00500' => array(
'gene_id' => 'PP00006G00500',
'e_value' => '3e-88',
'bit_score' => '293',
'alignment_length' => '554',
'identity_percentage' => '32.67',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'OS02G10350' => array(
'gene_id' => 'OS02G10350',
'e_value' => '1e-87',
'bit_score' => '286',
'alignment_length' => '475',
'identity_percentage' => '38.32',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'PP00296G00240' => array(
'gene_id' => 'PP00296G00240',
'e_value' => '3e-84',
'bit_score' => '279',
'alignment_length' => '483',
'identity_percentage' => '38.51',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'AT1G11000' => array(
'gene_id' => 'AT1G11000',
'e_value' => '4e-84',
'bit_score' => '280',
'alignment_length' => '477',
'identity_percentage' => '35.85',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
[maximum depth reached]
)
),
'PP00060G00990' => array(
'gene_id' => 'PP00060G00990',
'e_value' => '4e-76',
'bit_score' => '260',
'alignment_length' => '486',
'identity_percentage' => '34.36',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'PP00060G00970' => array(
'gene_id' => 'PP00060G00970',
'e_value' => '3e-66',
'bit_score' => '230',
'alignment_length' => '454',
'identity_percentage' => '35.46',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G00940' => array(
'gene_id' => 'ATR_00044G00940',
'e_value' => '9e-56',
'bit_score' => '194',
'alignment_length' => '213',
'identity_percentage' => '46.48',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OS05G34550' => array(
'gene_id' => 'OS05G34550',
'e_value' => '8e-55',
'bit_score' => '194',
'alignment_length' => '291',
'identity_percentage' => '41.92',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'OS04G58420' => array(
'gene_id' => 'OS04G58420',
'e_value' => '6e-39',
'bit_score' => '150',
'alignment_length' => '176',
'identity_percentage' => '40.91',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'OS02G35490' => array(
'gene_id' => 'OS02G35490',
'e_value' => '2e-35',
'bit_score' => '136',
'alignment_length' => '195',
'identity_percentage' => '42.05',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'OS06G40790' => array(
'gene_id' => 'OS06G40790',
'e_value' => '8e-32',
'bit_score' => '131',
'alignment_length' => '226',
'identity_percentage' => '35.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G01030' => array(
'gene_id' => 'ATR_00044G01030',
'e_value' => '5e-31',
'bit_score' => '125',
'alignment_length' => '237',
'identity_percentage' => '34.60',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'OT_13G00440' => array(
'gene_id' => 'OT_13G00440',
'e_value' => '1e-27',
'bit_score' => '122',
'alignment_length' => '471',
'identity_percentage' => '25.05',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
[maximum depth reached]
)
),
'OM_08G04030' => array(
'gene_id' => 'OM_08G04030',
'e_value' => '3e-25',
'bit_score' => '114',
'alignment_length' => '456',
'identity_percentage' => '26.10',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
[maximum depth reached]
)
),
'BPRRCC1105_02G06140' => array(
'gene_id' => 'BPRRCC1105_02G06140',
'e_value' => '3e-23',
'bit_score' => '108',
'alignment_length' => '334',
'identity_percentage' => '27.54',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
[maximum depth reached]
)
),
'OL13G00410' => array(
'gene_id' => 'OL13G00410',
'e_value' => '9e-22',
'bit_score' => '103',
'alignment_length' => '328',
'identity_percentage' => '28.35',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
[maximum depth reached]
)
),
'ORCC809_13G02620' => array(
'gene_id' => 'ORCC809_13G02620',
'e_value' => '1e-21',
'bit_score' => '103',
'alignment_length' => '328',
'identity_percentage' => '26.83',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_009G01200' => array(
'gene_id' => 'CNC64A_009G01200',
'e_value' => '3e-17',
'bit_score' => '89.0',
'alignment_length' => '429',
'identity_percentage' => '25.64',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
[maximum depth reached]
)
),
'ATR_00044G00930' => array(
'gene_id' => 'ATR_00044G00930',
'e_value' => '5e-17',
'bit_score' => '81.3',
'alignment_length' => '57',
'identity_percentage' => '68.42',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.11g01460' => array(
'gene_id' => 'RCC4223.11g01460',
'e_value' => '6e-17',
'bit_score' => '88.2',
'alignment_length' => '266',
'identity_percentage' => '28.95',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'PI00G12690' => array(
'gene_id' => 'PI00G12690',
'e_value' => '4e-16',
'bit_score' => '85.5',
'alignment_length' => '231',
'identity_percentage' => '29.87',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'VC00G46120' => array(
'gene_id' => 'VC00G46120',
'e_value' => '4e-15',
'bit_score' => '82.8',
'alignment_length' => '353',
'identity_percentage' => '24.36',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'PI00G23890' => array(
'gene_id' => 'PI00G23890',
'e_value' => '3e-14',
'bit_score' => '79.7',
'alignment_length' => '207',
'identity_percentage' => '28.02',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
[maximum depth reached]
)
),
'MRCC299_07G01620' => array(
'gene_id' => 'MRCC299_07G01620',
'e_value' => '8e-14',
'bit_score' => '78.2',
'alignment_length' => '196',
'identity_percentage' => '30.10',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
[maximum depth reached]
)
),
'RCC4223.03g08940' => array(
'gene_id' => 'RCC4223.03g08940',
'e_value' => '1e-13',
'bit_score' => '77.8',
'alignment_length' => '226',
'identity_percentage' => '28.32',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
[maximum depth reached]
)
),
'AC00G50730' => array(
'gene_id' => 'AC00G50730',
'e_value' => '1e-11',
'bit_score' => '71.2',
'alignment_length' => '250',
'identity_percentage' => '26.80',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
),
'AP00G43030' => array(
'gene_id' => 'AP00G43030',
'e_value' => '2e-10',
'bit_score' => '68.2',
'alignment_length' => '212',
'identity_percentage' => '29.25',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'AP00G35900' => array(
'gene_id' => 'AP00G35900',
'e_value' => '2e-09',
'bit_score' => '64.7',
'alignment_length' => '214',
'identity_percentage' => '28.50',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
[maximum depth reached]
)
),
'CR01G03670' => array(
'gene_id' => 'CR01G03670',
'e_value' => '4e-09',
'bit_score' => '63.9',
'alignment_length' => '186',
'identity_percentage' => '24.73',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
[maximum depth reached]
)
),
'VC00G12520' => array(
'gene_id' => 'VC00G12520',
'e_value' => '6e-09',
'bit_score' => '63.5',
'alignment_length' => '327',
'identity_percentage' => '25.38',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
[maximum depth reached]
)
),
'CNC64A_043G00190' => array(
'gene_id' => 'CNC64A_043G00190',
'e_value' => '2e-07',
'bit_score' => '57.8',
'alignment_length' => '242',
'identity_percentage' => '23.97',
'gf' => array(
[maximum depth reached]
)
),
'MP01G06640' => array(
'gene_id' => 'MP01G06640',
'e_value' => '6e-07',
'bit_score' => '56.2',
'alignment_length' => '182',
'identity_percentage' => '26.92',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
[maximum depth reached]
)
),
'AC00G50740' => array(
'gene_id' => 'AC00G50740',
'e_value' => '4e-06',
'bit_score' => '50.4',
'alignment_length' => '86',
'identity_percentage' => '32.56',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
[maximum depth reached]
)
)
),
'similarity_hits_species' => array(
'ath' => array(
(int) 0 => 'AT1G11310',
(int) 1 => 'AT1G61560',
(int) 2 => 'AT2G39200',
(int) 3 => 'AT2G17480',
(int) 4 => 'AT2G33670',
(int) 5 => 'AT3G45290',
(int) 6 => 'AT5G65970',
(int) 7 => 'AT2G17430',
(int) 8 => 'AT1G42560',
(int) 9 => 'AT2G44110',
(int) 10 => 'AT4G02600',
(int) 11 => 'AT4G24250',
(int) 12 => 'AT1G26700',
(int) 13 => 'AT5G53760',
(int) 14 => 'AT1G11000'
),
'atr' => array(
(int) 0 => 'ATR_00034G00450',
(int) 1 => 'ATR_00044G01050',
(int) 2 => 'ATR_00108G00260',
(int) 3 => 'ATR_00061G00090',
(int) 4 => 'ATR_00066G00720',
(int) 5 => 'ATR_00009G03790',
(int) 6 => 'ATR_00070G00670',
(int) 7 => 'ATR_00044G01020',
(int) 8 => 'ATR_00044G00940',
(int) 9 => 'ATR_00044G01030',
(int) 10 => 'ATR_00044G00930'
),
'osa' => array(
(int) 0 => 'OS03G03700',
(int) 1 => 'OS06G29110',
(int) 2 => 'OS10G39520',
(int) 3 => 'OS01G66510',
(int) 4 => 'OS04G36680',
(int) 5 => 'OS05G09050',
(int) 6 => 'OS11G07912',
(int) 7 => 'OS02G10350',
(int) 8 => 'OS05G34550',
(int) 9 => 'OS04G58420',
(int) 10 => 'OS02G35490',
(int) 11 => 'OS06G40790'
),
'ppa' => array(
(int) 0 => 'PP00210G00390',
(int) 1 => 'PP00122G00590',
(int) 2 => 'PP00024G00070',
(int) 3 => 'PP00060G01010',
(int) 4 => 'PP00403G00240',
(int) 5 => 'PP00099G00630',
(int) 6 => 'PP00012G00320',
(int) 7 => 'PP00006G00500',
(int) 8 => 'PP00296G00240',
(int) 9 => 'PP00060G00990',
(int) 10 => 'PP00060G00970'
),
'ota' => array(
(int) 0 => 'OT_13G00440'
),
'ome' => array(
(int) 0 => 'OM_08G04030'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_02G06140'
),
'olu' => array(
(int) 0 => 'OL13G00410'
),
'orcc809' => array(
(int) 0 => 'ORCC809_13G02620'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_009G01200'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.11g01460',
(int) 1 => 'RCC4223.03g08940'
),
'pse3' => array(
(int) 0 => 'PI00G12690',
(int) 1 => 'PI00G23890'
),
'vca' => array(
(int) 0 => 'VC00G46120',
(int) 1 => 'VC00G12520'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_07G01620'
),
'acg' => array(
(int) 0 => 'AC00G50730',
(int) 1 => 'AC00G50740'
),
'apr' => array(
(int) 0 => 'AP00G43030',
(int) 1 => 'AP00G35900'
),
'cre' => array(
(int) 0 => 'CR01G03670'
),
'mpu' => array(
(int) 0 => 'MP01G06640'
)
),
'gene_id' => 'AT1G11310',
'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' => 'AT1G11310',
'data_type' => 'gene_id',
'allow_async_use' => true,
'gene_placeholder' => 'WBGene00021049',
'gf_placeholder' => 'HOM03P008896',
'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(
'AT1G11310' => array(
'gene_id' => 'AT1G11310',
'e_value' => '0.0',
'bit_score' => '1186',
'alignment_length' => '574',
'identity_percentage' => '100.00',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT1G61560' => array(
'gene_id' => 'AT1G61560',
'e_value' => '0.0',
'bit_score' => '897',
'alignment_length' => '592',
'identity_percentage' => '76.18',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT2G39200' => array(
'gene_id' => 'AT2G39200',
'e_value' => '0.0',
'bit_score' => '819',
'alignment_length' => '587',
'identity_percentage' => '68.31',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'ATR_00034G00450' => array(
'gene_id' => 'ATR_00034G00450',
'e_value' => '0.0',
'bit_score' => '680',
'alignment_length' => '601',
'identity_percentage' => '57.07',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'OS03G03700' => array(
'gene_id' => 'OS03G03700',
'e_value' => '0.0',
'bit_score' => '529',
'alignment_length' => '521',
'identity_percentage' => '53.17',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'ATR_00044G01050' => array(
'gene_id' => 'ATR_00044G01050',
'e_value' => '1e-176',
'bit_score' => '518',
'alignment_length' => '576',
'identity_percentage' => '49.48',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'ATR_00108G00260' => array(
'gene_id' => 'ATR_00108G00260',
'e_value' => '5e-166',
'bit_score' => '491',
'alignment_length' => '508',
'identity_percentage' => '48.43',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P156863'
)
),
'OS06G29110' => array(
'gene_id' => 'OS06G29110',
'e_value' => '3e-157',
'bit_score' => '468',
'alignment_length' => '508',
'identity_percentage' => '47.83',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT2G17480' => array(
'gene_id' => 'AT2G17480',
'e_value' => '4e-146',
'bit_score' => '441',
'alignment_length' => '571',
'identity_percentage' => '42.73',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT2G33670' => array(
'gene_id' => 'AT2G33670',
'e_value' => '4e-144',
'bit_score' => '433',
'alignment_length' => '480',
'identity_percentage' => '46.25',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT3G45290' => array(
'gene_id' => 'AT3G45290',
'e_value' => '1e-143',
'bit_score' => '432',
'alignment_length' => '487',
'identity_percentage' => '42.09',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P148497'
)
),
'AT5G65970' => array(
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'e_value' => '4e-141',
'bit_score' => '428',
'alignment_length' => '540',
'identity_percentage' => '43.52',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT2G17430' => array(
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'e_value' => '1e-138',
'bit_score' => '421',
'alignment_length' => '470',
'identity_percentage' => '46.38',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'AT1G42560' => array(
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'e_value' => '5e-135',
'bit_score' => '408',
'alignment_length' => '461',
'identity_percentage' => '47.07',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'OS10G39520' => array(
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'e_value' => '1e-123',
'bit_score' => '380',
'alignment_length' => '420',
'identity_percentage' => '47.62',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006038'
)
),
'ATR_00061G00090' => array(
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'e_value' => '2e-120',
'bit_score' => '373',
'alignment_length' => '476',
'identity_percentage' => '42.65',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'ATR_00066G00720' => array(
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'e_value' => '3e-120',
'bit_score' => '372',
'alignment_length' => '518',
'identity_percentage' => '40.73',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'OS01G66510' => array(
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'bit_score' => '370',
'alignment_length' => '483',
'identity_percentage' => '41.41',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'AT2G44110' => array(
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'e_value' => '2e-119',
'bit_score' => '369',
'alignment_length' => '484',
'identity_percentage' => '41.74',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'AT4G02600' => array(
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'e_value' => '3e-115',
'bit_score' => '360',
'alignment_length' => '491',
'identity_percentage' => '42.16',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'AT4G24250' => array(
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'e_value' => '3e-115',
'bit_score' => '358',
'alignment_length' => '490',
'identity_percentage' => '41.43',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'ATR_00009G03790' => array(
'gene_id' => 'ATR_00009G03790',
'e_value' => '8e-108',
'bit_score' => '341',
'alignment_length' => '572',
'identity_percentage' => '36.89',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'PP00210G00390' => array(
'gene_id' => 'PP00210G00390',
'e_value' => '4e-105',
'bit_score' => '335',
'alignment_length' => '495',
'identity_percentage' => '38.18',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'AT1G26700' => array(
'gene_id' => 'AT1G26700',
'e_value' => '2e-103',
'bit_score' => '330',
'alignment_length' => '512',
'identity_percentage' => '38.09',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'OS04G36680' => array(
'gene_id' => 'OS04G36680',
'e_value' => '7e-100',
'bit_score' => '318',
'alignment_length' => '454',
'identity_percentage' => '42.51',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P169369'
)
),
'AT5G53760' => array(
'gene_id' => 'AT5G53760',
'e_value' => '1e-99',
'bit_score' => '321',
'alignment_length' => '475',
'identity_percentage' => '37.47',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'PP00122G00590' => array(
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'e_value' => '2e-99',
'bit_score' => '320',
'alignment_length' => '497',
'identity_percentage' => '38.63',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'PP00024G00070' => array(
'gene_id' => 'PP00024G00070',
'e_value' => '3e-97',
'bit_score' => '314',
'alignment_length' => '498',
'identity_percentage' => '38.55',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'ATR_00070G00670' => array(
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'e_value' => '6e-95',
'bit_score' => '308',
'alignment_length' => '473',
'identity_percentage' => '36.79',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P038392'
)
),
'ATR_00044G01020' => array(
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'e_value' => '8e-95',
'bit_score' => '299',
'alignment_length' => '298',
'identity_percentage' => '55.03',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P194291'
)
),
'PP00060G01010' => array(
'gene_id' => 'PP00060G01010',
'e_value' => '2e-94',
'bit_score' => '308',
'alignment_length' => '516',
'identity_percentage' => '35.66',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'OS05G09050' => array(
'gene_id' => 'OS05G09050',
'e_value' => '3e-94',
'bit_score' => '300',
'alignment_length' => '309',
'identity_percentage' => '47.25',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'PP00403G00240' => array(
'gene_id' => 'PP00403G00240',
'e_value' => '2e-93',
'bit_score' => '305',
'alignment_length' => '476',
'identity_percentage' => '36.97',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'PP00099G00630' => array(
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'e_value' => '8e-93',
'bit_score' => '303',
'alignment_length' => '563',
'identity_percentage' => '38.01',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'OS11G07912' => array(
'gene_id' => 'OS11G07912',
'e_value' => '9e-93',
'bit_score' => '300',
'alignment_length' => '495',
'identity_percentage' => '34.55',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P038392'
)
),
'PP00012G00320' => array(
'gene_id' => 'PP00012G00320',
'e_value' => '3e-90',
'bit_score' => '295',
'alignment_length' => '502',
'identity_percentage' => '35.46',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'PP00006G00500' => array(
'gene_id' => 'PP00006G00500',
'e_value' => '3e-88',
'bit_score' => '293',
'alignment_length' => '554',
'identity_percentage' => '32.67',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'OS02G10350' => array(
'gene_id' => 'OS02G10350',
'e_value' => '1e-87',
'bit_score' => '286',
'alignment_length' => '475',
'identity_percentage' => '38.32',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P122700'
)
),
'PP00296G00240' => array(
'gene_id' => 'PP00296G00240',
'e_value' => '3e-84',
'bit_score' => '279',
'alignment_length' => '483',
'identity_percentage' => '38.51',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'AT1G11000' => array(
'gene_id' => 'AT1G11000',
'e_value' => '4e-84',
'bit_score' => '280',
'alignment_length' => '477',
'identity_percentage' => '35.85',
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P038392'
)
),
'PP00060G00990' => array(
'gene_id' => 'PP00060G00990',
'e_value' => '4e-76',
'bit_score' => '260',
'alignment_length' => '486',
'identity_percentage' => '34.36',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P009924'
)
),
'PP00060G00970' => array(
'gene_id' => 'PP00060G00970',
'e_value' => '3e-66',
'bit_score' => '230',
'alignment_length' => '454',
'identity_percentage' => '35.46',
'species' => 'ppa',
'common_name' => 'Physcomitrella patens',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P191922'
)
),
'ATR_00044G00940' => array(
'gene_id' => 'ATR_00044G00940',
'e_value' => '9e-56',
'bit_score' => '194',
'alignment_length' => '213',
'identity_percentage' => '46.48',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P186901'
)
),
'OS05G34550' => array(
'gene_id' => 'OS05G34550',
'e_value' => '8e-55',
'bit_score' => '194',
'alignment_length' => '291',
'identity_percentage' => '41.92',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P038706'
)
),
'OS04G58420' => array(
'gene_id' => 'OS04G58420',
'e_value' => '6e-39',
'bit_score' => '150',
'alignment_length' => '176',
'identity_percentage' => '40.91',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P135994'
)
),
'OS02G35490' => array(
'gene_id' => 'OS02G35490',
'e_value' => '2e-35',
'bit_score' => '136',
'alignment_length' => '195',
'identity_percentage' => '42.05',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P115802'
)
),
'OS06G40790' => array(
'gene_id' => 'OS06G40790',
'e_value' => '8e-32',
'bit_score' => '131',
'alignment_length' => '226',
'identity_percentage' => '35.40',
'species' => 'osa',
'common_name' => 'Oryza sativa',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P181184'
)
),
'ATR_00044G01030' => array(
'gene_id' => 'ATR_00044G01030',
'e_value' => '5e-31',
'bit_score' => '125',
'alignment_length' => '237',
'identity_percentage' => '34.60',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P080727'
)
),
'OT_13G00440' => array(
'gene_id' => 'OT_13G00440',
'e_value' => '1e-27',
'bit_score' => '122',
'alignment_length' => '471',
'identity_percentage' => '25.05',
'species' => 'ota',
'common_name' => 'Ostreococcus tauri',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'OM_08G04030' => array(
'gene_id' => 'OM_08G04030',
'e_value' => '3e-25',
'bit_score' => '114',
'alignment_length' => '456',
'identity_percentage' => '26.10',
'species' => 'ome',
'common_name' => 'Ostreococcus mediterraneus',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'BPRRCC1105_02G06140' => array(
'gene_id' => 'BPRRCC1105_02G06140',
'e_value' => '3e-23',
'bit_score' => '108',
'alignment_length' => '334',
'identity_percentage' => '27.54',
'species' => 'bprrcc1105',
'common_name' => 'Bathycoccus prasinos',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'OL13G00410' => array(
'gene_id' => 'OL13G00410',
'e_value' => '9e-22',
'bit_score' => '103',
'alignment_length' => '328',
'identity_percentage' => '28.35',
'species' => 'olu',
'common_name' => 'Ostreococcus lucimarinus',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'ORCC809_13G02620' => array(
'gene_id' => 'ORCC809_13G02620',
'e_value' => '1e-21',
'bit_score' => '103',
'alignment_length' => '328',
'identity_percentage' => '26.83',
'species' => 'orcc809',
'common_name' => 'Ostreococcus sp RCC809',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'CNC64A_009G01200' => array(
'gene_id' => 'CNC64A_009G01200',
'e_value' => '3e-17',
'bit_score' => '89.0',
'alignment_length' => '429',
'identity_percentage' => '25.64',
'species' => 'cnc64a',
'common_name' => 'Chlorella sp NC64A',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P016075'
)
),
'ATR_00044G00930' => array(
'gene_id' => 'ATR_00044G00930',
'e_value' => '5e-17',
'bit_score' => '81.3',
'alignment_length' => '57',
'identity_percentage' => '68.42',
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P099355'
)
),
'RCC4223.11g01460' => array(
'gene_id' => 'RCC4223.11g01460',
'e_value' => '6e-17',
'bit_score' => '88.2',
'alignment_length' => '266',
'identity_percentage' => '28.95',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'PI00G12690' => array(
'gene_id' => 'PI00G12690',
'e_value' => '4e-16',
'bit_score' => '85.5',
'alignment_length' => '231',
'identity_percentage' => '29.87',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'VC00G46120' => array(
'gene_id' => 'VC00G46120',
'e_value' => '4e-15',
'bit_score' => '82.8',
'alignment_length' => '353',
'identity_percentage' => '24.36',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P006909'
)
),
'PI00G23890' => array(
'gene_id' => 'PI00G23890',
'e_value' => '3e-14',
'bit_score' => '79.7',
'alignment_length' => '207',
'identity_percentage' => '28.02',
'species' => 'pse3',
'common_name' => 'Picochlorum sp. SENEW3 (SE3)',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'MRCC299_07G01620' => array(
'gene_id' => 'MRCC299_07G01620',
'e_value' => '8e-14',
'bit_score' => '78.2',
'alignment_length' => '196',
'identity_percentage' => '30.10',
'species' => 'mrcc299',
'common_name' => 'Micromonas sp RCC299',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P064501'
)
),
'RCC4223.03g08940' => array(
'gene_id' => 'RCC4223.03g08940',
'e_value' => '1e-13',
'bit_score' => '77.8',
'alignment_length' => '226',
'identity_percentage' => '28.32',
'species' => 'prcc4223',
'common_name' => 'Picochlorum_RCC4223',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'AC00G50730' => array(
'gene_id' => 'AC00G50730',
'e_value' => '1e-11',
'bit_score' => '71.2',
'alignment_length' => '250',
'identity_percentage' => '26.80',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P131296'
)
),
'AP00G43030' => array(
'gene_id' => 'AP00G43030',
'e_value' => '2e-10',
'bit_score' => '68.2',
'alignment_length' => '212',
'identity_percentage' => '29.25',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'AP00G35900' => array(
'gene_id' => 'AP00G35900',
'e_value' => '2e-09',
'bit_score' => '64.7',
'alignment_length' => '214',
'identity_percentage' => '28.50',
'species' => 'apr',
'common_name' => 'Auxenochlorella protothecoides',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P067884'
)
),
'CR01G03670' => array(
'gene_id' => 'CR01G03670',
'e_value' => '4e-09',
'bit_score' => '63.9',
'alignment_length' => '186',
'identity_percentage' => '24.73',
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P196749'
)
),
'VC00G12520' => array(
'gene_id' => 'VC00G12520',
'e_value' => '6e-09',
'bit_score' => '63.5',
'alignment_length' => '327',
'identity_percentage' => '25.38',
'species' => 'vca',
'common_name' => 'Volvox carteri',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P191262'
)
),
'CNC64A_043G00190' => array(
'gene_id' => 'CNC64A_043G00190',
'e_value' => '2e-07',
'bit_score' => '57.8',
'alignment_length' => '242',
'identity_percentage' => '23.97',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
),
'MP01G06640' => array(
'gene_id' => 'MP01G06640',
'e_value' => '6e-07',
'bit_score' => '56.2',
'alignment_length' => '182',
'identity_percentage' => '26.92',
'species' => 'mpu',
'common_name' => 'Micromonas pusilla strain CCMP1545',
'gf' => array(
'HOMFAM' => 'HOM03P000896',
'ORTHOFAM' => 'ORTHO03P064501'
)
),
'AC00G50740' => array(
'gene_id' => 'AC00G50740',
'e_value' => '4e-06',
'bit_score' => '50.4',
'alignment_length' => '86',
'identity_percentage' => '32.56',
'species' => 'acg',
'common_name' => 'Asterochloris sp. Cgr-DA1pho v2.0',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P038706'
)
)
)
$similarity_hits_species = array(
'ath' => array(
(int) 0 => 'AT1G11310',
(int) 1 => 'AT1G61560',
(int) 2 => 'AT2G39200',
(int) 3 => 'AT2G17480',
(int) 4 => 'AT2G33670',
(int) 5 => 'AT3G45290',
(int) 6 => 'AT5G65970',
(int) 7 => 'AT2G17430',
(int) 8 => 'AT1G42560',
(int) 9 => 'AT2G44110',
(int) 10 => 'AT4G02600',
(int) 11 => 'AT4G24250',
(int) 12 => 'AT1G26700',
(int) 13 => 'AT5G53760',
(int) 14 => 'AT1G11000'
),
'atr' => array(
(int) 0 => 'ATR_00034G00450',
(int) 1 => 'ATR_00044G01050',
(int) 2 => 'ATR_00108G00260',
(int) 3 => 'ATR_00061G00090',
(int) 4 => 'ATR_00066G00720',
(int) 5 => 'ATR_00009G03790',
(int) 6 => 'ATR_00070G00670',
(int) 7 => 'ATR_00044G01020',
(int) 8 => 'ATR_00044G00940',
(int) 9 => 'ATR_00044G01030',
(int) 10 => 'ATR_00044G00930'
),
'osa' => array(
(int) 0 => 'OS03G03700',
(int) 1 => 'OS06G29110',
(int) 2 => 'OS10G39520',
(int) 3 => 'OS01G66510',
(int) 4 => 'OS04G36680',
(int) 5 => 'OS05G09050',
(int) 6 => 'OS11G07912',
(int) 7 => 'OS02G10350',
(int) 8 => 'OS05G34550',
(int) 9 => 'OS04G58420',
(int) 10 => 'OS02G35490',
(int) 11 => 'OS06G40790'
),
'ppa' => array(
(int) 0 => 'PP00210G00390',
(int) 1 => 'PP00122G00590',
(int) 2 => 'PP00024G00070',
(int) 3 => 'PP00060G01010',
(int) 4 => 'PP00403G00240',
(int) 5 => 'PP00099G00630',
(int) 6 => 'PP00012G00320',
(int) 7 => 'PP00006G00500',
(int) 8 => 'PP00296G00240',
(int) 9 => 'PP00060G00990',
(int) 10 => 'PP00060G00970'
),
'ota' => array(
(int) 0 => 'OT_13G00440'
),
'ome' => array(
(int) 0 => 'OM_08G04030'
),
'bprrcc1105' => array(
(int) 0 => 'BPRRCC1105_02G06140'
),
'olu' => array(
(int) 0 => 'OL13G00410'
),
'orcc809' => array(
(int) 0 => 'ORCC809_13G02620'
),
'cnc64a' => array(
(int) 0 => 'CNC64A_009G01200'
),
'prcc4223' => array(
(int) 0 => 'RCC4223.11g01460',
(int) 1 => 'RCC4223.03g08940'
),
'pse3' => array(
(int) 0 => 'PI00G12690',
(int) 1 => 'PI00G23890'
),
'vca' => array(
(int) 0 => 'VC00G46120',
(int) 1 => 'VC00G12520'
),
'mrcc299' => array(
(int) 0 => 'MRCC299_07G01620'
),
'acg' => array(
(int) 0 => 'AC00G50730',
(int) 1 => 'AC00G50740'
),
'apr' => array(
(int) 0 => 'AP00G43030',
(int) 1 => 'AP00G35900'
),
'cre' => array(
(int) 0 => 'CR01G03670'
),
'mpu' => array(
(int) 0 => 'MP01G06640'
)
)
$gene_id = 'AT1G11310'
$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 = 'AT1G11310'
$data_type = 'gene_id'
$allow_async_use = true
$gene_placeholder = 'WBGene00021049'
$gf_placeholder = 'HOM03P008896'
$title_for_layout = 'Pico-PLAZA 3.0 : Interactive Phylogenetics Module'
$collapse1 = ''
$collapse2 = 'collapse in'
$similarity_hit = array(
'gene_id' => 'CNC64A_043G00190',
'e_value' => '2e-07',
'bit_score' => '57.8',
'alignment_length' => '242',
'identity_percentage' => '23.97',
'gf' => array(
'HOMFAM' => 'HOM03P007606',
'ORTHOFAM' => 'ORTHO03P011524'
)
)
$checked = null
$similarity_hit_gene = 'CNC64A_043G00190'
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-07 |
57.8 |
242 |
23.97 |