Phylota table contains all sequence, cluster and taxonomic information from a phylotaR pipeline run.
Usage
# S4 method for class 'Phylota'
as.character(x)
# S4 method for class 'Phylota'
show(object)
# S4 method for class 'Phylota'
print(x)
# S4 method for class 'Phylota'
str(object, max.level = 2L, ...)
# S4 method for class 'Phylota'
summary(object)
# S4 method for class 'Phylota,character'
x[[i]]Slots
cidsIDs of all clusters
sidsIDs of all sequences
txidsIDs of all taxa
sqsAll sequence records as SeqArc
clstrsAll cluster records as ClstrArc
txdctTaxonomic dictionary as TaxDict
prnt_idParent taxonomic ID
prnt_nmParent taxonomic name
See also
Other run-public:
ClstrArc-class,
ClstrRec-class,
SeqArc-class,
SeqRec-class,
TaxDict-class,
TaxRec-class,
clusters2_run(),
clusters_run(),
parameters_reset(),
reset(),
restart(),
run(),
setup(),
taxise_run()
Examples
data('aotus')
# this is a Phylota object
# it contains cluster, sequence and taxonomic information from a phylotaR run
show(aotus)
#> Phylota Table (Aotus)
#> - [184] clusters
#> - [1945] sequences
#> - [13] source taxa
# you can access its different data slots with @
aotus@cids # cluster IDs
#> [1] "0" "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11"
#> [13] "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23"
#> [25] "24" "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35"
#> [37] "36" "37" "38" "39" "40" "41" "42" "43" "44" "45" "46" "47"
#> [49] "48" "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59"
#> [61] "60" "61" "62" "63" "64" "65" "66" "67" "68" "69" "70" "71"
#> [73] "72" "73" "74" "75" "76" "77" "78" "79" "80" "81" "82" "83"
#> [85] "84" "85" "86" "87" "88" "89" "90" "91" "92" "93" "94" "95"
#> [97] "96" "97" "98" "99" "100" "101" "102" "103" "104" "105" "106" "107"
#> [109] "108" "109" "110" "111" "112" "113" "114" "115" "116" "117" "118" "119"
#> [121] "120" "121" "122" "123" "124" "125" "126" "127" "128" "129" "130" "131"
#> [133] "132" "133" "134" "135" "136" "137" "138" "139" "140" "141" "142" "143"
#> [145] "144" "145" "146" "147" "148" "149" "150" "151" "152" "153" "154" "155"
#> [157] "156" "157" "158" "159" "160" "161" "162" "163" "164" "165" "166" "167"
#> [169] "168" "169" "170" "171" "172" "173" "174" "175" "176" "177" "178" "179"
#> [181] "180" "181" "182" "183"
aotus@sids # sequence IDs
#> [1] "KR528418.1" "JF444279.1" "AY227074.1" "AY227073.1" "AY227072.1"
#> [6] "AY227071.1" "AY227070.1" "AY227069.1" "AY227068.1" "AY227067.1"
#> [11] "AY227066.1" "AY227065.1" "AY227064.1" "AY227063.1" "AY227062.1"
#> [16] "AY227061.1" "AY227060.1" "AY227059.1" "AY227058.1" "AY227057.1"
#> [21] "AY227056.1" "AY227055.1" "DQ321669.1" "MW327030.1" "MT489117.1"
#> [26] "MT489116.1" "MT489115.1" "MT489114.1" "MT489113.1" "MT489112.1"
#> [31] "MT489111.1" "MT489110.1" "MT489075.1" "MT489074.1" "MT489073.1"
#> [36] "MT489072.1" "MT489071.1" "MT489070.1" "MT489069.1" "MT489068.1"
#> [41] "MT489032.1" "MT489031.1" "MT489030.1" "MT489029.1" "MT489028.1"
#> [46] "MT489027.1" "MT489026.1" "MT489025.1" "MT488990.1" "MT488989.1"
#> [51] "MT488988.1" "MT488987.1" "MT488986.1" "MT488985.1" "MT488984.1"
#> [56] "MT488983.1" "MT488947.1" "MT488946.1" "MT488945.1" "MT488944.1"
#> [61] "MT488943.1" "MT488942.1" "MT488941.1" "MT488940.1" "MT488904.1"
#> [66] "MT488903.1" "MT488902.1" "MT488901.1" "MT488900.1" "MT488899.1"
#> [71] "MT488898.1" "MT488897.1" "MT488861.1" "MT488860.1" "MT488859.1"
#> [76] "MT488858.1" "MT488857.1" "MT488856.1" "MT488855.1" "MT488854.1"
#> [81] "MT488815.1" "MT488814.1" "MT488813.1" "MT488812.1" "MT488811.1"
#> [86] "MT488810.1" "MT488809.1" "MT488808.1" "MT488778.1" "MT488777.1"
#> [91] "MT488776.1" "MT488775.1" "MT488774.1" "MT488773.1" "MT488772.1"
#> [96] "MT488771.1" "MT488734.1" "MT488733.1" "MT488732.1" "MT488731.1"
#> [101] "MT488730.1" "MT488729.1" "MT488728.1" "MT488727.1" "MT488672.1"
#> [106] "MT488671.1" "MT488670.1" "MT488669.1" "MT488659.1" "MT488658.1"
#> [111] "MT488657.1" "MT488569.1" "MT488568.1" "MT488567.1" "MT488566.1"
#> [116] "MF632281.1" "MF632280.1" "KX774456.1" "KR902344.1" "DQ321666.1"
#> [121] "DQ321665.1" "DQ162635.1" "DQ162634.1" "DQ162633.1" "DQ162630.1"
#> [126] "DQ162629.1" "DQ162628.1" "DQ162627.1" "DQ162626.1" "DQ162624.1"
#> [131] "AY563263.2" "AY563258.2" "AY563227.2" "AY563219.2" "AY659834.1"
#> [136] "AY659833.1" "AY659832.1" "AY659831.1" "AY659830.1" "AY659829.1"
#> [141] "AF352260.1" "AF352259.1" "AF014508.1" "AF014507.1" "AF014506.1"
#> [146] "AF014504.1" "HQ005503.1" "HQ005502.1" "HQ018928.1" "AY114539.1"
#> [151] "AY114538.1" "AY114537.1" "AY114536.1" "AY114535.1" "AY114534.1"
#> [156] "AY114533.1" "AY114532.1" "AY114531.1" "AY114530.1" "AY114529.1"
#> [161] "KC762196.1" "KC762163.1" "KC762106.1" "KC762075.1" "KC762017.1"
#> [166] "KC761983.1" "KC761954.1" "KC761921.1" "KC761892.1" "KC761836.1"
#> [171] "KC761816.1" "KC761785.1" "KC761698.1" "KC761635.1" "KC761604.1"
#> [176] "KC761572.1" "KC761540.1" "KC761507.1" "KC761473.1" "KC761408.1"
#> [181] "KC761373.1" "KC761279.1" "KC761245.1" "KC761212.1" "KC761180.1"
#> [186] "KC761083.1" "KC761053.1" "KC761019.1" "KC760991.1" "MW736163.1"
#> [191] "MT489140.1" "MT489139.1" "MT489137.1" "MT489136.1" "MT489135.1"
#> [196] "MT489134.1" "MT489095.1" "MT489094.1" "MT489092.1" "MT489091.1"
#> [201] "MT489053.1" "MT489052.1" "MT489050.1" "MT489049.1" "MT489048.1"
#> [206] "MT489010.1" "MT489009.1" "MT489007.1" "MT489006.1" "MT488968.1"
#> [211] "MT488967.1" "MT488965.1" "MT488964.1" "MT488963.1" "MT488925.1"
#> [216] "MT488924.1" "MT488922.1" "MT488921.1" "MT488920.1" "MT488882.1"
#> [221] "MT488881.1" "MT488879.1" "MT488878.1" "MT488839.1" "MT488838.1"
#> [226] "MT488800.1" "MT488799.1" "MT488797.1" "MT488796.1" "MT488795.1"
#> [231] "MT488756.1" "MT488755.1" "MT488753.1" "MT488752.1" "MT488751.1"
#> [236] "MT488681.1" "MT488680.1" "MT488679.1" "MT488678.1" "MT488677.1"
#> [241] "MT488676.1" "MT488592.1" "MT488591.1" "MT488589.1" "MT488588.1"
#> [246] "MT488587.1" "MT488586.1" "MT492189.1" "MT492188.1" "MT483740.1"
#> [251] "MT483739.1" "MT483737.1" "MT483736.1" "MT483735.1" "MT483734.1"
#> [256] "MF615381.1" "MF615380.1" "MF615379.1" "MF615378.1" "MF615377.1"
#> [261] "MF615376.1" "MK205145.1" "MF632285.1" "MF632284.1" "MF632283.1"
#> [266] "MF632282.1" "MW736164.1" "MT489147.1" "MT489141.1" "MT489126.1"
#> [271] "MT489106.1" "MT489102.1" "MT489096.1" "MT489083.1" "MT489064.1"
#> [276] "MT489060.1" "MT489054.1" "MT489040.1" "MT489021.1" "MT489017.1"
#> [281] "MT489011.1" "MT488998.1" "MT488979.1" "MT488975.1" "MT488969.1"
#> [286] "MT488955.1" "MT488936.1" "MT488926.1" "MT488912.1" "MT488893.1"
#> [291] "MT488889.1" "MT488883.1" "MT488870.1" "MT488850.1" "MT488846.1"
#> [296] "MT488840.1" "MT488831.1" "MT488807.1" "MT488801.1" "MT488787.1"
#> [301] "MT488767.1" "MT488763.1" "MT488757.1" "MT488743.1" "MT488723.1"
#> [306] "MT488675.1" "MT488655.1" "MT488599.1" "MT488593.1" "MT488578.1"
#> [311] "MT488558.1" "MT492196.1" "MT492190.1" "MT492179.1" "MT483747.1"
#> [316] "MT483741.1" "MT483726.1" "MT483706.1" "DQ321664.1" "DQ162736.1"
#> [321] "DQ162732.1" "DQ162729.1" "DQ162727.1" "DQ162719.1" "DQ162718.1"
#> [326] "DQ162711.1" "DQ162710.1" "AY563262.2" "AY563261.2" "AY563260.2"
#> [331] "AY563259.2" "AY563257.2" "AY563256.2" "AY563254.2" "AY563253.2"
#> [336] "AY563252.2" "AY563251.2" "AY563250.2" "AY563249.2" "AY563248.2"
#> [341] "AY563247.2" "AY563246.2" "AY563245.2" "AY563244.2" "AY563243.2"
#> [346] "AY563242.2" "AY563241.2" "AY563229.2" "AY563226.2" "AY659828.1"
#> [351] "AY659827.1" "AY659826.1" "AF352258.1" "AF352257.1" "AF352256.1"
#> [356] "AF132757.1" "AF129797.1" "AF097328.1" "AF097326.1" "AF097324.1"
#> [361] "JQ932319.1" "JQ932318.1" "JQ932310.1" "JQ932304.1" "JQ932303.1"
#> [366] "JQ932293.1" "JQ932280.1" "JQ932259.1" "JQ932255.1" "JQ932245.1"
#> [371] "JQ932232.1" "JQ932362.1" "JQ932359.1" "JQ932356.1" "JQ932605.1"
#> [376] "JQ932597.1" "JQ932590.1" "JQ932717.1" "JQ932662.1" "JQ932636.1"
#> [381] "JQ932630.1" "JQ932822.1" "JQ932821.1" "JQ932818.1" "JQ932817.1"
#> [386] "JQ932816.1" "JQ932815.1" "JQ932814.1" "JQ932813.1" "JQ932812.1"
#> [391] "JQ932809.1" "JQ932807.1" "JQ932806.1" "JQ932805.1" "JQ932804.1"
#> [396] "JQ932803.1" "JQ932802.1" "JQ932801.1" "JQ932800.1" "JQ932799.1"
#> [401] "JQ932794.1" "JQ932775.1" "JQ932756.1" "JQ932751.1" "JQ932724.1"
#> [406] "JQ932932.1" "JQ932931.1" "JQ932930.1" "JQ932929.1" "JQ932928.1"
#> [411] "JQ932927.1" "JQ932926.1" "JQ932925.1" "JQ932924.1" "JQ932923.1"
#> [416] "JQ932922.1" "JQ932921.1" "JQ932920.1" "JQ932918.1" "JQ932916.1"
#> [421] "JQ932914.1" "JQ932913.1" "JQ932909.1" "JQ932908.1" "JQ932905.1"
#> [426] "JQ932903.1" "JQ932897.1" "JQ932896.1" "JQ932895.1" "JQ932892.1"
#> [431] "JQ932891.1" "JQ932890.1" "JQ932889.1" "JQ932888.1" "JQ932887.1"
#> [436] "JQ932886.1" "JQ932885.1" "JQ932884.1" "JQ932882.1" "JQ932881.1"
#> [441] "JQ932880.1" "JQ932879.1" "JQ932877.1" "JQ932874.1" "JQ932873.1"
#> [446] "JQ932872.1" "JQ932870.1" "JQ932869.1" "JQ932868.1" "JQ932867.1"
#> [451] "JQ932866.1" "JQ932865.1" "JQ932864.1" "JQ932863.1" "JQ932862.1"
#> [456] "JQ932861.1" "JQ932859.1" "JQ932857.1" "JQ932856.1" "JQ932855.1"
#> [461] "JQ932854.1" "JQ932853.1" "JQ932852.1" "JQ932851.1" "JQ932850.1"
#> [466] "JQ932849.1" "JQ932847.1" "JQ932846.1" "JQ932845.1" "JQ932844.1"
#> [471] "JQ932843.1" "JQ932842.1" "JQ932841.1" "JQ932840.1" "JQ932839.1"
#> [476] "JQ932838.1" "JQ932837.1" "JQ932836.1" "JQ932835.1" "JQ932833.1"
#> [481] "JQ932831.1" "JQ932830.1" "JQ932829.1" "JQ932827.1" "JQ932823.1"
#> [486] "JQ933029.1" "JQ933028.1" "JQ933027.1" "JQ933026.1" "JQ933023.1"
#> [491] "JQ933020.1" "JQ933011.1" "JQ933006.1" "JQ933005.1" "JQ933004.1"
#> [496] "JQ933001.1" "JQ933000.1" "JQ932999.1" "JQ932998.1" "JQ932997.1"
#> [501] "JQ932996.1" "JQ932995.1" "JQ932994.1" "JQ932993.1" "JQ932992.1"
#> [506] "JQ932991.1" "JQ932990.1" "JQ932989.1" "JQ932988.1" "JQ932987.1"
#> [511] "JQ932986.1" "JQ932985.1" "JQ932984.1" "JQ932983.1" "JQ932982.1"
#> [516] "JQ932981.1" "JQ932980.1" "JQ932979.1" "JQ932978.1" "JQ932977.1"
#> [521] "JQ932976.1" "JQ932975.1" "JQ932974.1" "JQ932973.1" "JQ932972.1"
#> [526] "JQ932971.1" "JQ932970.1" "JQ932969.1" "JQ932967.1" "JQ932966.1"
#> [531] "JQ932965.1" "JQ932964.1" "JQ932963.1" "JQ932962.1" "JQ932961.1"
#> [536] "JQ932960.1" "JQ932959.1" "JQ932958.1" "JQ932957.1" "JQ932956.1"
#> [541] "JQ932955.1" "JQ932954.1" "JQ932953.1" "JQ932934.1" "JQ932933.1"
#> [546] "JQ963361.1" "JQ963360.1" "JQ963351.1" "JQ963350.1" "JQ963349.1"
#> [551] "JQ963348.1" "JQ963347.1" "JQ963346.1" "JQ933101.1" "JQ933099.1"
#> [556] "JQ933082.1" "JQ933076.1" "JQ933075.1" "JQ933053.1" "MT489118.1"
#> [561] "MT489076.1" "MT489033.1" "MT488991.1" "MT488948.1" "MT488905.1"
#> [566] "MT488862.1" "MT488816.1" "MT488779.1" "MT488735.1" "MT488656.1"
#> [571] "MT488570.1" "MT492172.1" "MT483718.1" "MT253565.1" "MT232916.1"
#> [576] "MT232915.1" "LR699078.1" "LR699077.1" "LR699076.1" "LS481196.1"
#> [581] "LS481195.1" "LS481194.1" "LS481193.1" "LS481192.1" "AF097329.1"
#> [586] "AF097327.1" "AF097325.1" "AF097321.1" "JN161047.1" "HQ005506.1"
#> [591] "HQ018927.1" "KC762193.1" "KC762160.1" "KC762127.1" "KC762104.1"
#> [596] "KC762072.1" "KC762014.1" "KC761980.1" "KC761951.1" "KC761918.1"
#> [601] "KC761889.1" "KC761833.1" "KC761813.1" "KC761782.1" "KC761755.1"
#> [606] "KC761695.1" "KC761632.1" "KC761601.1" "KC761569.1" "KC761537.1"
#> [611] "KC761504.1" "KC761470.1" "KC761438.1" "KC761405.1" "KC761371.1"
#> [616] "KC761338.1" "KC761242.1" "KC761210.1" "KC761177.1" "KC761144.1"
#> [621] "KC761111.1" "KC761080.1" "KC761050.1" "KC761016.1" "KC760988.1"
#> [626] "KC760954.1" "KC760891.1" "KC760866.1" "KC760833.1" "KC760802.1"
#> [631] "KC760770.1" "KC760738.1" "KC760712.1" "KC760681.1" "KC760646.1"
#> [636] "KC760611.1" "KC760576.1" "KC760514.1" "KC760483.1" "KC760450.1"
#> [641] "KC760417.1" "KC760385.1" "KC760326.1" "KC760263.1" "KC760228.1"
#> [646] "KC761952.1" "KC761919.1" "KC761890.1" "KC761834.1" "KC761814.1"
#> [651] "KC761783.1" "KC761756.1" "KC761696.1" "KC761633.1" "KC761602.1"
#> [656] "KC761570.1" "KC761538.1" "KC761505.1" "KC761471.1" "KC761439.1"
#> [661] "KC761406.1" "KC761339.1" "KC761277.1" "KC761243.1" "KC761178.1"
#> [666] "KC761145.1" "KC761081.1" "KC761051.1" "KC761017.1" "KC760989.1"
#> [671] "KC760955.1" "KC760892.1" "KC760867.1" "KC760834.1" "KC760803.1"
#> [676] "KC760771.1" "KC760739.1" "KC760713.1" "KC760682.1" "KC760647.1"
#> [681] "KC760612.1" "KC760577.1" "KC760515.1" "KC760484.1" "KC760451.1"
#> [686] "KC760418.1" "KC760386.1" "KC760327.1" "KC760264.1" "KC760229.1"
#> [691] "AY225808.2" "AY225809.2" "AF169487.1" "AF169486.1" "AF169485.1"
#> [696] "U36770.1" "HM756840.1" "HM757383.1" "HM757558.1" "HM757724.1"
#> [701] "HM758216.1" "HM758297.1" "HM758465.1" "HM758650.1" "HM758934.1"
#> [706] "HM759105.1" "HM759278.1" "HM759372.1" "HM759646.1" "HM759729.1"
#> [711] "HM759896.1" "HM760080.1" "HM760256.1" "HM760529.1" "HM760608.1"
#> [716] "HM760775.1" "HM761013.1" "HM761145.1" "HM761195.1" "HM761507.1"
#> [721] "HM761772.1" "HM761929.1" "HM762096.1" "HM762207.1" "HM762431.1"
#> [726] "HM762511.1" "HM762768.1" "HM762858.1" "HM763021.1" "HM763265.1"
#> [731] "HM763433.1" "HM763726.1" "HM763996.1" "HM764104.1" "HM764321.1"
#> [736] "HM764396.1" "HM764648.1" "AF185631.1" "AF185630.1" "AF185629.1"
#> [741] "AF185628.1" "AF185627.1" "AF185625.1" "AF185624.1" "AF185623.1"
#> [746] "AF107758.1" "AF107755.1" "AF107753.1" "AF107750.1" "AF107749.1"
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#> [1616] "MT488933.1" "MT488931.1" "MT488930.1" "MT488929.1" "MT488928.1"
#> [1621] "MT488919.1" "MT488918.1" "MT488916.1" "MT488915.1" "MT488914.1"
#> [1626] "MT488913.1" "MT488909.1" "MT488896.1" "MT488894.1" "MT488892.1"
#> [1631] "MT488891.1" "MT488890.1" "MT488888.1" "MT488887.1" "MT488886.1"
#> [1636] "MT488885.1" "MT488877.1" "MT488876.1" "MT488875.1" "MT488874.1"
#> [1641] "MT488873.1" "MT488872.1" "MT488871.1" "MT488867.1" "MT488853.1"
#> [1646] "MT488852.1" "MT488851.1" "MT488849.1" "MT488848.1" "MT488847.1"
#> [1651] "MT488845.1" "MT488844.1" "MT488843.1" "MT488842.1" "MT488836.1"
#> [1656] "MT488835.1" "MT488834.1" "MT488833.1" "MT488832.1" "MT488830.1"
#> [1661] "MT488829.1" "MT488826.1" "MT488822.1" "MT488821.1" "MT488820.1"
#> [1666] "MT488819.1" "MT488818.1" "MT488817.1" "MT488806.1" "MT488805.1"
#> [1671] "MT488804.1" "MT488803.1" "MT488794.1" "MT488793.1" "MT488792.1"
#> [1676] "MT488791.1" "MT488790.1" "MT488789.1" "MT488788.1" "MT488784.1"
#> [1681] "MT488770.1" "MT488769.1" "MT488768.1" "MT488766.1" "MT488765.1"
#> [1686] "MT488764.1" "MT488762.1" "MT488761.1" "MT488760.1" "MT488759.1"
#> [1691] "MT488750.1" "MT488749.1" "MT488748.1" "MT488747.1" "MT488746.1"
#> [1696] "MT488745.1" "MT488744.1" "MT488740.1" "MT488726.1" "MT488725.1"
#> [1701] "MT488724.1" "MT488722.1" "MT488721.1" "MT488720.1" "MT489146.1"
#> [1706] "MT489145.1" "MT489144.1" "MT489143.1" "MT489133.1" "MT489132.1"
#> [1711] "MT489131.1" "MT489130.1" "MT489129.1" "MT489128.1" "MT489127.1"
#> [1716] "MT489123.1" "MT489109.1" "MT489108.1" "MT489107.1" "MT489105.1"
#> [1721] "MT489104.1" "MT489103.1" "MT489101.1" "MT489100.1" "MT489099.1"
#> [1726] "MT489098.1" "MT489090.1" "MT489089.1" "MT489088.1" "MT489087.1"
#> [1731] "MT489086.1" "MT489085.1" "MT489084.1" "MT489080.1" "MT489067.1"
#> [1736] "MT489066.1" "MT489065.1" "MT489063.1" "MT489062.1" "MT489061.1"
#> [1741] "MT489059.1" "MT489058.1" "MT489057.1" "MT489056.1" "MT489047.1"
#> [1746] "MT489046.1" "MT489045.1" "MT489044.1" "MT489043.1" "MT489042.1"
#> [1751] "MT489041.1" "MT489037.1" "MT489024.1" "MT489023.1" "MT489022.1"
#> [1756] "MT489020.1" "MT489019.1" "MT489018.1" "MT489016.1" "MT489015.1"
#> [1761] "MT489014.1" "MT489013.1" "MT489005.1" "MT489004.1" "MT489003.1"
#> [1766] "MT489002.1" "MT489001.1" "MT489000.1" "MT488999.1" "MT488995.1"
#> [1771] "MT488982.1" "MT488981.1" "MT488980.1" "MT488978.1" "MT488977.1"
#> [1776] "MT488976.1" "MT488974.1" "MT488973.1" "MT488972.1" "MT488971.1"
#> [1781] "MT488962.1" "MT488961.1" "MT488960.1" "MT488959.1" "MT488958.1"
#> [1786] "MT488957.1" "MT488956.1" "MT488952.1" "HM761930.1" "HM762097.1"
#> [1791] "HM762245.1" "HM762432.1" "HM762516.1" "HM762770.1" "HM762862.1"
#> [1796] "HM763022.1" "HM763266.1" "HM763434.1" "HM763727.1" "HM763997.1"
#> [1801] "HM764105.1" "HM764322.1" "HM764401.1" "HM764649.1" "HM764817.1"
#> [1806] "HM764908.1" "HM765180.1" "U38998.1" "AY684995.1" "AY684994.1"
#> [1811] "AY684993.1" "AY684992.1" "AY684991.1" "AY646200.1" "AY646198.1"
#> [1816] "DM461196.1" "DM461195.1" "DM461194.1" "DM461193.1" "DM461192.1"
#> [1821] "DM461191.1" "DM367551.1" "DM367548.1" "DM367545.1" "DM367544.1"
#> [1826] "DM367543.1" "DM367542.1" "DM367541.1" "DM367540.1" "DM371283.1"
#> [1831] "DM371280.1" "DM371276.1" "DM371275.1" "DM371274.1" "DM371273.1"
#> [1836] "DM371272.1" "DM371271.1" "DQ334827.1" "HW478258.1" "HW478257.1"
#> [1841] "HW478256.1" "HW478255.1" "DI178960.1" "DI178959.1" "DI178958.1"
#> [1846] "DI178957.1" "DI178956.1" "DI178955.1" "DI178127.1" "DI178124.1"
#> [1851] "DI178120.1" "DI178119.1" "DI178118.1" "DI178117.1" "DI178116.1"
#> [1856] "DI178115.1" "AB239248.1" "AB239247.1" "AB239246.1" "AB239228.1"
#> [1861] "AB239227.1" "AB239226.1" "AB239203.1" "AB239202.1" "AB239201.1"
#> [1866] "AB239200.1" "U59646.1" "U59645.1" "U59644.1" "AF161947.1"
#> [1871] "AF161946.1" "HM756841.1" "HM757384.1" "HM757559.1" "HM757725.1"
#> [1876] "HM758217.1" "HM758302.1" "HM758466.1" "HM758655.1" "HM758935.1"
#> [1881] "HM759106.1" "HM759279.1" "HM759377.1" "HM759647.1" "HM759819.1"
#> [1886] "HM759901.1" "HM760085.1" "HM760261.1" "HM760530.1" "HM760613.1"
#> [1891] "HM760776.1" "HM761014.1" "HM761146.1" "HM761196.1" "HM761512.1"
#> [1896] "HM761773.1" "MT489142.1" "MT489097.1" "MT489055.1" "MT489012.1"
#> [1901] "MT488970.1" "MT488927.1" "MT488884.1" "MT488841.1" "MT488802.1"
#> [1906] "MT488758.1" "MT488674.1" "MT488594.1" "MT492191.1" "MT483742.1"
#> [1911] "KY508415.1" "KY508414.1" "KY508413.1" "KY508412.1" "KY508411.1"
#> [1916] "KY508410.1" "KY508409.1" "KY508408.1" "KY508407.1" "KY508406.1"
#> [1921] "KY508405.1" "KY508404.1" "FJ154795.1" "FJ154794.1" "FJ154793.1"
#> [1926] "DQ098874.1" "DQ098873.1" "DQ098862.1" "DQ098861.1" "AY894656.1"
#> [1931] "AY894655.1" "AY894654.1" "AY894653.1" "AY894652.1" "AY894651.1"
#> [1936] "AY894650.1" "AY894649.1" "AY894648.1" "AY894647.1" "HQ005499.1"
#> [1941] "HQ018926.1" "HM102288.1" "AF004921.1" "HW478260.1" "HW478259.1"
aotus@txids # taxonomic IDs
#> [1] "231953" "1002694" "361674" "292213" "57176" "57175" "43147"
#> [8] "37293" "280755" "867331" "30591" "120088" "9505"
aotus@clstrs # clusters archive
#> Archive of cluster record(s)
#> - [184] clusters
aotus@sqs # sequence archive
#> Archive of sequence record(s)
#> - [1945] sequences
#> - [13] unique txids
#> - [597] median sequence length
#> - [0] median ambiguous nucleotides
aotus@txdct # taxonomic dictionary
#> Taxonomic dictionary [22] recs, parent [id 9504]
# see all of the available slots
(slotNames(aotus))
#> [1] "cids" "txids" "sids" "txdct" "sqs" "clstrs" "prnt_id"
#> [8] "prnt_nm"
# access different sequences and clusters with [[
(aotus[['0']]) # cluster record 0
#> Cluster Record [id 0]
#> - [subtree] type
#> - [AF129795.1] seed sequence
#> - [173] sequences
#> - [5] taxa
(aotus[[aotus@sids[[1]]]]) # first sequence record
#> SeqRec [ID: KR528418.1]
# get a summary of the whole object
(summary(aotus))
#> ID Type Seed Parent N_taxa N_seqs Med_sql MAD
#> 1 0 subtree AF129795.1 9504 5 173 266.0 0.7090455
#> 2 1 subtree DQ098863.1 9504 10 66 1140.0 0.8966920
#> 3 2 subtree AY659849.1 9504 5 55 1071.0 0.8062280
#> 4 3 subtree DI178118.1 9504 2 52 267.0 0.8666904
#> 5 4 subtree LC075891.1 9504 2 50 844.0 0.8244061
#> 6 5 subtree HM761925.1 9504 9 49 710.0 0.9581328
#> 7 6 subtree HM763429.1 9504 9 49 339.0 0.8417867
#> 8 7 subtree JQ933053.1 9504 9 48 582.5 0.6754071
#> 9 8 subtree HM759641.1 9504 9 48 272.0 0.8482955
#> 10 9 subtree KC761951.1 9504 9 47 649.0 0.9808119
#> 11 10 subtree MT489103.1 9504 8 45 1138.0 0.9992970
#> 12 11 subtree KC762127.1 9504 9 45 797.0 0.9619747
#> 13 12 subtree KC761371.1 9504 9 45 584.0 0.9551948
#> 14 13 subtree KC760228.1 9504 9 43 276.0 0.8748720
#> 15 14 subtree JQ932794.1 9504 4 43 568.0 0.6655075
#> 16 15 direct LC075891.1 30591 1 43 900.0 0.8328878
#> 17 16 subtree EF658652.1 9504 9 41 647.0 0.9793822
#> 18 17 subtree HM760775.1 9504 8 41 680.0 0.9590605
#> 19 18 subtree MT488555.1 9504 8 41 842.0 1.0000000
#> 20 19 subtree U38998.1 9504 8 40 618.0 0.4020846
#> 21 20 subtree DQ321662.1 9504 8 35 549.0 0.7988127
#> 22 21 subtree JQ932751.1 9504 2 35 796.0 0.7788508
#> 23 22 subtree JN161069.1 9504 1 30 1088.0 0.9985614
#> 24 23 direct LC456000.1 30591 1 30 795.0 0.7748913
#> 25 24 subtree JN161069.1 30591 1 30 1088.0 0.9985614
#> 26 25 subtree AF333711.1 9504 1 28 394.0 0.9228029
#> 27 26 subtree JQ932884.1 9504 4 24 757.5 0.8431763
#> 28 27 subtree LC075890.1 9504 2 24 850.0 0.8423276
#> 29 28 subtree DQ098867.1 30591 2 24 1140.0 0.9663743
#> 30 29 subtree AY900534.1 9504 1 21 291.0 0.8561767
#> 31 30 subtree AF378747.1 9504 1 20 364.0 0.8938575
#> 32 31 subtree AY227055.1 2688256 1 20 269.0 0.9722022
#> 33 32 subtree HM763430.1 30591 2 20 339.0 0.9353022
#> 34 33 subtree HM759643.1 30591 2 20 272.0 0.9726316
#> 35 34 subtree HM761926.1 30591 2 20 711.0 0.9638889
#> 36 35 subtree JQ932877.1 9504 4 19 521.0 0.8932277
#> 37 36 subtree JQ933028.1 9504 2 19 758.0 0.8135355
#> 38 37 subtree JQ932999.1 9504 1 18 633.0 0.6914067
#> 39 38 subtree AF027542.1 9504 1 18 287.0 0.8127515
#> 40 39 subtree AF333712.1 9504 1 18 378.0 0.9713542
#> 41 40 direct LC075890.1 30591 1 18 861.5 0.8424253
#> 42 41 subtree MT483703.1 30591 2 18 618.0 0.9973118
#> 43 42 subtree MT488555.1 30591 2 18 842.0 1.0000000
#> 44 43 subtree MT492158.1 30591 2 18 647.0 0.9997424
#> 45 44 subtree MT483753.1 30591 2 18 905.5 0.9994481
#> 46 45 subtree MT488933.1 30591 2 18 582.5 0.9780015
#> 47 46 subtree MT488817.1 30591 2 18 680.5 0.9938815
#> 48 47 subtree MT489103.1 30591 2 18 1138.0 1.0000000
#> 49 48 subtree MT489061.1 30591 2 18 807.5 0.9813448
#> 50 49 subtree MT489018.1 30591 2 18 649.0 0.9949727
#> 51 50 subtree MT488976.1 30591 2 18 584.0 0.9794101
#> 52 51 subtree JQ932845.1 9504 3 16 587.0 0.6638030
#> 53 52 subtree MT488890.1 30591 2 16 273.0 0.9650350
#> 54 53 subtree MF615377.1 9504 3 14 684.0 0.9140625
#> 55 54 direct LC456005.1 30591 1 14 732.5 0.7900048
#> 56 55 subtree DQ321662.1 30591 2 13 549.0 0.8050398
#> 57 56 subtree AF161946.1 9504 4 12 1059.0 0.9937048
#> 58 57 subtree JQ932800.1 9504 3 12 633.0 0.9001762
#> 59 58 subtree JQ932874.1 9504 1 12 543.5 0.8983452
#> 60 59 subtree KY508404.1 9504 1 12 411.5 0.9586317
#> 61 60 subtree JQ932840.1 9504 1 11 565.0 0.8977661
#> 62 61 subtree AF107750.1 9504 1 11 323.0 0.9789997
#> 63 62 subtree AY900546.1 9504 1 11 290.0 0.6960557
#> 64 63 subtree AY646200.1 9504 4 10 498.0 0.7077341
#> 65 64 subtree JQ932868.1 9504 2 10 561.0 0.8921095
#> 66 65 subtree AY894647.1 9504 1 10 1170.0 0.9992314
#> 67 66 subtree JQ932807.1 9504 1 9 637.0 0.7393674
#> 68 67 subtree AF338375.1 9504 6 8 829.0 0.9398372
#> 69 68 subtree JQ932913.1 9504 2 7 754.0 0.7807910
#> 70 69 subtree HM758650.1 9504 5 7 680.0 0.9595003
#> 71 70 subtree AY900559.1 9504 1 7 285.0 0.7339125
#> 72 71 direct EF658652.1 30591 1 7 629.0 0.9754224
#> 73 72 subtree JQ933020.1 9504 4 6 663.0 0.7837435
#> 74 73 subtree KC761051.1 9504 4 6 473.5 0.6571595
#> 75 74 subtree HM759273.1 9504 5 6 706.5 0.9834499
#> 76 75 subtree AY449069.1 9504 1 6 685.0 1.0000000
#> 77 76 subtree AY684991.1 9504 1 6 1618.0 0.7991497
#> 78 77 direct AY449069.1 30591 1 6 685.0 1.0000000
#> 79 78 subtree DQ989366.1 9504 5 5 428.0 0.9616822
#> 80 79 subtree JQ933005.1 9504 1 5 878.0 0.9155983
#> 81 80 subtree JQ932259.1 9504 1 5 868.0 0.9529944
#> 82 81 subtree JQ932880.1 9504 1 5 556.0 0.8463190
#> 83 82 subtree JQ932869.1 9504 3 5 464.0 0.9661795
#> 84 83 subtree HM756838.1 9504 5 5 549.0 0.9756708
#> 85 84 subtree HM757379.1 9504 5 5 612.0 0.9934641
#> 86 85 subtree HM757554.1 9504 5 5 475.0 0.9233684
#> 87 86 subtree HM757720.1 9504 5 5 898.0 0.9656766
#> 88 87 subtree HM758212.1 9504 5 5 342.0 0.9964912
#> 89 88 subtree HM758297.1 9504 5 5 637.0 0.9885626
#> 90 89 subtree HM758463.1 9504 5 5 590.0 0.9831405
#> 91 90 subtree HM758930.1 9504 5 5 507.0 0.7943343
#> 92 91 subtree HM759101.1 9504 5 5 1077.0 0.9996286
#> 93 92 subtree HM759372.1 9504 5 5 611.0 0.9716150
#> 94 93 subtree HM759729.1 9504 5 5 355.0 0.9684507
#> 95 94 subtree HM759896.1 9504 5 5 580.0 0.9466877
#> 96 95 subtree HM760080.1 9504 5 5 585.0 0.9125413
#> 97 96 subtree HM760256.1 9504 5 5 538.0 0.9951852
#> 98 97 subtree HM760525.1 9504 5 5 554.0 0.9806104
#> 99 98 subtree HM760608.1 9504 5 5 658.0 0.9900452
#> 100 99 subtree HM761193.1 9504 5 5 617.0 0.9765452
#> 101 100 subtree HM761507.1 9504 5 5 558.0 0.9528796
#> 102 101 subtree HM761768.1 9504 5 5 475.0 0.9436326
#> 103 102 subtree HM762092.1 9504 5 5 707.0 0.9786885
#> 104 103 subtree HM762180.1 9504 5 5 761.0 0.9842313
#> 105 104 subtree HM762427.1 9504 5 5 957.0 0.9610152
#> 106 105 subtree HM762765.1 9504 5 5 612.0 0.9719870
#> 107 106 subtree HM763261.1 9504 5 5 1000.0 0.9952000
#> 108 107 subtree HM763727.1 9504 5 5 1245.0 0.9358974
#> 109 108 subtree HM764102.1 9504 5 5 998.0 0.9961924
#> 110 109 subtree HM764317.1 9504 5 5 951.0 0.9501577
#> 111 110 subtree KR902342.1 9504 3 4 1374.0 1.0000000
#> 112 111 subtree AF014508.1 9504 4 4 446.0 0.9983221
#> 113 112 subtree AF014506.1 9504 4 4 312.5 0.9498480
#> 114 113 subtree KC762160.1 9504 4 4 748.0 0.9759680
#> 115 114 subtree KC762072.1 9504 4 4 576.0 0.8039153
#> 116 115 subtree KC762014.1 9504 4 4 663.0 0.9701046
#> 117 116 subtree KC761980.1 9504 4 4 616.5 0.9772000
#> 118 117 subtree KC761918.1 9504 4 4 776.0 0.9932778
#> 119 118 subtree KC761889.1 9504 4 4 522.0 0.9976099
#> 120 119 subtree KC761833.1 9504 4 4 660.0 0.9840504
#> 121 120 subtree KC761782.1 9504 4 4 668.0 0.9589872
#> 122 121 subtree KC761695.1 9504 4 4 735.0 0.8670848
#> 123 122 subtree KC761632.1 9504 4 4 707.0 0.9679219
#> 124 123 subtree KC761601.1 9504 4 4 425.0 0.9982394
#> 125 124 subtree KC761569.1 9504 4 4 744.5 0.9476667
#> 126 125 subtree KC761504.1 9504 4 4 660.0 0.7352784
#> 127 126 subtree KC761470.1 9504 4 4 969.5 0.8648844
#> 128 127 subtree KC761405.1 9504 4 4 459.5 0.8912338
#> 129 128 subtree KC761242.1 9504 4 4 674.0 0.9823529
#> 130 129 subtree KC761177.1 9504 4 4 679.5 0.9255830
#> 131 130 subtree KC761016.1 9504 4 4 445.0 0.9786996
#> 132 131 subtree KC760988.1 9504 4 4 362.0 0.9559229
#> 133 132 subtree JQ932280.1 9504 3 4 554.5 0.7425948
#> 134 133 subtree JQ932662.1 9504 3 4 684.0 0.8431659
#> 135 134 subtree HM762511.1 9504 4 4 521.5 0.9765326
#> 136 135 subtree HM764645.1 9504 4 4 643.5 0.9519231
#> 137 136 subtree AF027546.1 9504 1 4 287.5 0.8907186
#> 138 137 subtree HM764908.1 9504 4 4 490.5 0.9909091
#> 139 138 subtree HM765175.1 9504 4 4 370.0 0.8861985
#> 140 139 subtree AB239200.1 9504 1 4 587.0 0.9995741
#> 141 140 direct DQ098863.1 30591 1 4 1140.0 1.0000000
#> 142 141 direct DQ098851.1 30591 1 4 498.0 1.0000000
#> 143 142 subtree HM758657.1 30591 2 4 679.5 0.9992647
#> 144 143 subtree MW321653.1 9504 2 3 1666.0 0.9988017
#> 145 144 subtree AF014509.1 9504 3 3 343.0 1.0000000
#> 146 145 subtree KC762104.1 9504 3 3 566.0 0.9878261
#> 147 146 subtree KC761277.1 9504 3 3 467.0 0.9775439
#> 148 147 subtree KC761210.1 9504 3 3 386.0 0.8732158
#> 149 148 subtree KC761755.1 9504 3 3 905.0 0.8968421
#> 150 149 subtree KC761438.1 9504 3 3 594.0 0.9977591
#> 151 150 subtree KC761338.1 9504 3 3 538.0 0.9725777
#> 152 151 subtree KC760954.1 9504 3 3 449.0 0.8990349
#> 153 152 subtree KC760866.1 9504 3 3 475.0 0.9845614
#> 154 153 subtree KC760833.1 9504 3 3 527.0 0.9829222
#> 155 154 subtree KC760802.1 9504 3 3 461.0 0.9885305
#> 156 155 subtree KC760770.1 9504 3 3 668.0 0.9736457
#> 157 156 subtree KC760738.1 9504 3 3 518.0 0.9589552
#> 158 157 subtree KC760712.1 9504 3 3 314.0 0.9681529
#> 159 158 subtree KC760681.1 9504 3 3 683.0 0.8234416
#> 160 159 subtree KC760611.1 9504 3 3 531.0 0.9924953
#> 161 160 subtree KC760514.1 9504 3 3 482.0 0.9965565
#> 162 161 subtree KC760417.1 9504 3 3 557.0 0.9976062
#> 163 162 subtree KC760385.1 9504 3 3 420.0 1.0000000
#> 164 163 subtree KC760326.1 9504 3 3 464.0 0.9737589
#> 165 164 subtree KC760263.1 9504 3 3 475.0 0.9971989
#> 166 165 subtree HM761011.1 9504 3 3 764.0 0.9973856
#> 167 166 subtree HM761143.1 9504 3 3 802.0 0.9995844
#> 168 167 subtree HM762858.1 9504 3 3 624.0 0.9941706
#> 169 168 subtree HM763019.1 9504 3 3 431.0 0.9783449
#> 170 169 subtree HM763994.1 9504 3 3 778.0 0.9961489
#> 171 170 subtree HM764396.1 9504 3 3 530.0 1.0000000
#> 172 171 subtree AY900524.1 9504 1 3 366.0 0.7523810
#> 173 172 subtree HM764813.1 9504 3 3 575.0 0.9884660
#> 174 173 subtree AY449065.1 9504 1 3 666.0 0.9980010
#> 175 174 subtree AY449057.1 9504 1 3 667.0 1.0000000
#> 176 175 subtree HM756999.1 9504 3 3 837.0 0.9890325
#> 177 176 subtree AB239246.1 9504 1 3 616.0 0.9989195
#> 178 177 subtree AB239226.1 9504 1 3 614.0 0.9994571
#> 179 178 subtree FJ154793.1 9504 1 3 890.0 0.9992509
#> 180 179 direct AY449065.1 30591 1 3 666.0 0.9980010
#> 181 180 direct AY449057.1 30591 1 3 667.0 1.0000000
#> 182 181 direct MF632276.1 30591 1 3 1059.0 1.0000000
#> 183 182 subtree HM759274.1 30591 2 3 695.0 0.9904489
#> 184 183 subtree AF338376.1 30591 2 3 829.0 1.0000000
#> Definition Feature
#> 1 aotus (0.07), partial (0.07) -
#> 2 aotus (0.1), cds (0.1) -
#> 3 aotus (0.09), class (0.09) -
#> 4 antibody (0.05), construct (0.05) jp (0.3), kr (0.2)
#> 5 dna (0.1), aotus (0.1) -
#> 6 aotus (0.1), fbn1 (0.1) -
#> 7 aotus (0.09), chrna1 (0.09) -
#> 8 aotus (0.1), genomic (0.1) -
#> 9 aotus (0.1), gene (0.1) -
#> 10 aotus (0.1), genomic (0.1) -
#> 11 gene (0.2), complete (0.1) -
#> 12 aotus (0.1), genomic (0.1) -
#> 13 aotus (0.1), genomic (0.1) -
#> 14 aotus (0.1), genomic (0.1) -
#> 15 aotus (0.2), genomic (0.2) -
#> 16 dna (0.2), aotus (0.1) -
#> 17 aotus (0.09), cds (0.09) barcode (1)
#> 18 aotus (0.1), gene (0.1) -
#> 19 atp (0.1), f0 (0.1) -
#> 20 gene (0.08), sequence (0.08) -
#> 21 gene (0.09), mitochondrial (0.09) -
#> 22 aotus (0.1), azarai (0.1) -
#> 23 azarai (0.2), aotus (0.1) -
#> 24 aotus (0.1), azarai (0.1) -
#> 25 azarai (0.2), aotus (0.1) -
#> 26 aotus (0.08), cds (0.08) -
#> 27 aotus (0.2), genomic (0.2) -
#> 28 aotus (0.2), azarai (0.1) -
#> 29 aotus (0.1), cds (0.1) -
#> 30 aotus (0.08), chain (0.08) -
#> 31 aotus (0.08), cds (0.08) -
#> 32 antigen (0.08), aotus (0.08) -
#> 33 aotus (0.09), azarai (0.09) -
#> 34 aotus (0.1), azarai (0.1) -
#> 35 aotus (0.1), azarai (0.1) -
#> 36 aotus (0.2), genomic (0.2) -
#> 37 aotus (0.2), azarai (0.1) -
#> 38 aotus (0.2), genomic (0.2) -
#> 39 alpha (0.09), aotus (0.09) -
#> 40 aotus (0.09), cds (0.09) -
#> 41 aotus (0.2), azarai (0.2) -
#> 42 aotus (0.08), azarai (0.08) -
#> 43 atp (0.1), f0 (0.1) -
#> 44 aotus (0.08), azarai (0.08) -
#> 45 aotus (0.08), azarai (0.08) -
#> 46 aotus (0.1), azarai (0.1) -
#> 47 aotus (0.1), azarai (0.1) -
#> 48 gene (0.2), complete (0.1) -
#> 49 aotus (0.1), azarai (0.1) -
#> 50 aotus (0.1), azarai (0.1) -
#> 51 aotus (0.1), azarai (0.1) -
#> 52 aotus (0.2), genomic (0.2) -
#> 53 aotus (0.1), azarai (0.1) -
#> 54 allele (0.08), aotus (0.08) -
#> 55 aotus (0.2), azarai (0.2) -
#> 56 azarai (0.1), gene (0.08) -
#> 57 aotus (0.09), cc (0.09) -
#> 58 aotus (0.2), genomic (0.2) -
#> 59 aotus (0.2), genomic (0.2) -
#> 60 sequence (0.2), aotus (0.1) -
#> 61 aotus (0.2), genomic (0.2) -
#> 62 aotus (0.08), beta (0.08) -
#> 63 aotus (0.08), cds (0.08) -
#> 64 aotus (0.1), cds (0.1) -
#> 65 aotus (0.2), genomic (0.2) -
#> 66 aotus (0.1), clone (0.1) -
#> 67 aotus (0.2), genomic (0.2) -
#> 68 sry (0.2), aotus (0.1) -
#> 69 aotus (0.2), genomic (0.2) -
#> 70 aotus (0.1), gene (0.1) -
#> 71 aotus (0.08), cds (0.08) -
#> 72 aotus (0.08), azarai (0.08) -
#> 73 aotus (0.2), genomic (0.2) -
#> 74 aotus (0.2), genomic (0.2) -
#> 75 aotus (0.1), dennd5a (0.1) -
#> 76 azarai (0.1), clone (0.1) -
#> 77 aotus (0.1), cds (0.1) -
#> 78 azarai (0.1), clone (0.1) -
#> 79 aotus (0.1), cds (0.1) -
#> 80 aotus (0.2), genomic (0.2) -
#> 81 aotus (0.2), genomic (0.2) -
#> 82 aotus (0.2), genomic (0.2) -
#> 83 aotus (0.2), genomic (0.2) -
#> 84 aotus (0.1), gene (0.1) -
#> 85 aotus (0.1), gene (0.1) -
#> 86 aotus (0.1), gene (0.1) -
#> 87 aotus (0.1), gene (0.1) -
#> 88 aotus (0.1), gene (0.1) -
#> 89 aotus (0.1), gene (0.1) -
#> 90 aotus (0.1), gene (0.1) -
#> 91 aotus (0.1), gene (0.1) -
#> 92 aotus (0.1), gene (0.1) -
#> 93 aotus (0.1), gene (0.1) -
#> 94 aotus (0.1), gene (0.1) -
#> 95 aotus (0.1), gene (0.1) -
#> 96 aotus (0.1), gene (0.1) -
#> 97 aotus (0.1), gene (0.1) -
#> 98 aotus (0.1), gene (0.1) -
#> 99 aotus (0.1), gene (0.1) -
#> 100 aotus (0.1), gene (0.1) -
#> 101 aotus (0.1), foxp1 (0.1) -
#> 102 aotus (0.1), fes (0.1) -
#> 103 aotus (0.1), fam123b (0.1) -
#> 104 aotus (0.1), erc2 (0.1) -
#> 105 aotus (0.1), edg1 (0.1) -
#> 106 aotus (0.1), dctn2 (0.1) -
#> 107 aotus (0.1), cnr1 (0.1) -
#> 108 aotus (0.1), brca2 (0.1) -
#> 109 aotus (0.1), bche (0.1) -
#> 110 aotus (0.1), axin1 (0.1) -
#> 111 cd4 (0.2), aotus (0.1) -
#> 112 alpha (0.1), aotus (0.1) -
#> 113 aotus (0.1), cds (0.1) -
#> 114 aotus (0.2), genomic (0.2) -
#> 115 aotus (0.2), genomic (0.2) -
#> 116 aotus (0.2), genomic (0.2) -
#> 117 aotus (0.2), genomic (0.2) -
#> 118 aotus (0.2), genomic (0.2) -
#> 119 aotus (0.2), genomic (0.2) -
#> 120 aotus (0.2), genomic (0.2) -
#> 121 aotus (0.2), genomic (0.2) -
#> 122 aotus (0.2), genomic (0.2) -
#> 123 aotus (0.2), genomic (0.2) -
#> 124 aotus (0.2), genomic (0.2) -
#> 125 aotus (0.2), genomic (0.2) -
#> 126 aotus (0.2), genomic (0.2) -
#> 127 aotus (0.2), genomic (0.2) -
#> 128 aotus (0.2), genomic (0.2) -
#> 129 aotus (0.2), genomic (0.2) -
#> 130 aotus (0.2), genomic (0.2) -
#> 131 aotus (0.2), genomic (0.2) -
#> 132 aotus (0.2), genomic (0.2) -
#> 133 aotus (0.2), genomic (0.2) -
#> 134 aotus (0.2), genomic (0.2) -
#> 135 aotus (0.1), dmrt1 (0.1) -
#> 136 aotus (0.1), app (0.1) -
#> 137 alpha (0.09), aotus (0.09) -
#> 138 aff2 (0.1), aotus (0.1) -
#> 139 adora3 (0.1), aotus (0.1) -
#> 140 aotus (0.1), dna (0.1) -
#> 141 aotus (0.1), azarai (0.1) -
#> 142 aotus (0.1), azarai (0.1) -
#> 143 aotus (0.1), azarai (0.1) -
#> 144 aotus (0.1), cds (0.1) -
#> 145 aotus (0.1), cds (0.1) -
#> 146 aotus (0.2), genomic (0.2) -
#> 147 aotus (0.2), genomic (0.2) -
#> 148 aotus (0.2), genomic (0.2) -
#> 149 aotus (0.2), genomic (0.2) -
#> 150 aotus (0.2), genomic (0.2) -
#> 151 aotus (0.2), genomic (0.2) -
#> 152 aotus (0.2), genomic (0.2) -
#> 153 aotus (0.2), genomic (0.2) -
#> 154 aotus (0.2), genomic (0.2) -
#> 155 aotus (0.2), genomic (0.2) -
#> 156 aotus (0.2), genomic (0.2) -
#> 157 aotus (0.2), genomic (0.2) -
#> 158 aotus (0.2), genomic (0.2) -
#> 159 aotus (0.2), genomic (0.2) -
#> 160 aotus (0.2), genomic (0.2) -
#> 161 aotus (0.2), genomic (0.2) -
#> 162 aotus (0.2), genomic (0.2) -
#> 163 aotus (0.2), genomic (0.2) -
#> 164 aotus (0.2), genomic (0.2) -
#> 165 aotus (0.2), genomic (0.2) -
#> 166 aotus (0.1), gene (0.1) -
#> 167 aotus (0.1), gene (0.1) -
#> 168 aotus (0.1), dach1 (0.1) -
#> 169 aotus (0.1), crem (0.1) -
#> 170 aotus (0.1), bcor (0.1) -
#> 171 aotus (0.1), atxn7 (0.1) -
#> 172 aotus (0.08), cds (0.08) -
#> 173 aff22 (0.1), aotus (0.1) -
#> 174 autos (0.1), azarai (0.1) -
#> 175 autos (0.1), azarai (0.1) -
#> 176 aotus (0.1), azarai (0.1) -
#> 177 aotus (0.1), dna (0.1) -
#> 178 aotus (0.1), dna (0.1) -
#> 179 aotus (0.08), cds (0.08) -
#> 180 autos (0.1), azarai (0.1) -
#> 181 autos (0.1), azarai (0.1) -
#> 182 aotus (0.1), azarai (0.1) -
#> 183 aotus (0.1), azarai (0.1) -
#> 184 sry (0.2), aotus (0.1) -
# the above generates a data.frame with information on each cluster:
# ID - unique id in the object
# Type - cluster type
# Seed - most connected sequence
# Parent - MRCA of all represented taxa
# N_taxa - number of NCBI recognised taxa
# N_seqs - number of sequences
# Med_sql - median sequence length
# MAD - Maximum alignment density, values close to 1 indicate all sequences in
# the cluster have a similar length.
# Definition - most common words (and frequency) in sequence definitions
# Feature - most common feature name (and frequency)