1
$\begingroup$

I ran PorthoMCL but I could not find an explanation about the output format and I would like to visualise the results, maybe as a circos plot. PorthoMCL produces two output files:

To create the above outputs they used 12 genes as input.

Here are the first 5 lines of each file to illustrate the format:

  1. Orthologs

    NC_000913|NP_416270.1   NC_000916|NP_276057.1   NC_000913|NP_415023.1   NC_000916|NP_275620.1   NC_000913|NP_416372.1   NC_000916|NP_275748.1   NC_000913|NP_418459.1   NC_000913|NP_415400.1   NC_000916|NP_275839.1   NC_000913|YP_026282.1   NC_000913|NP_415281.1   NC_000913|NP_415120.1   NC_000916|NP_276816.1   NC_000913|NP_415635.4   NC_000913|NP_415958.1   NC_000913|NP_417907.2   NC_000916|NP_276221.1   NC_000913|NP_414796.2   NC_000913|NP_415028.1   NC_000913|NP_416705.2   NC_000913|NP_417937.1   NC_000913|NP_416000.1   NC_000916|NP_275276.1   NC_000913|YP_025300.1   NC_000913|NP_416809.1   NC_000913|NP_415315.4   NC_000916|NP_276601.1   NC_000913|NP_415807.1   NC_000916|NP_276150.1   NC_000913|NP_414669.1   NC_000913|NP_417997.1   NC_000913|NP_415286.1   NC_000913|NP_417668.1   NC_000913|NP_414900.1   NC_000913|NP_414693.1   NC_000913|NP_415644.1   NC_000913|NP_415453.1   NC_000913|NP_415385.1   NC_000913|NP_417737.1   NC_000913|NP_416224.1   NC_000913|NP_416685.1   NC_000913|NP_415763.1   NC_000913|NP_417163.1   NC_000913|NP_415185.1   NC_000913|NP_416917.1   NC_000913|NP_416001.1   NC_000916|NP_276486.1   NC_000913|NP_414741.1   NC_000913|NP_415330.1   NC_000913|NP_416427.1   NC_000913|NP_415376.4   NC_000913|YP_026225.1   NC_000913|NP_418707.1   NC_000913|NP_417998.1   NC_000913|NP_414608.1   NC_000913|NP_415350.2   NC_000913|NP_418520.1   NC_000913|NP_415806.1   NC_000913|NP_416633.1   NC_000913|NP_417920.1   NC_000913|NP_417936.1   NC_000913|NP_418530.1   NC_002570|NP_243996.1   NC_002570|NP_244512.1   NC_002570|NP_242964.1   NC_002570|NP_242329.1   NC_002570|NP_241947.1   NC_002570|NP_244161.1   NC_002570|NP_244348.1   NC_002570|NP_244469.1   NC_002570|NP_241038.1   NC_002570|NP_241216.1   NC_002570|NP_241378.1   NC_002570|NP_242006.1   NC_002570|NP_244540.1   NC_002570|NP_244761.1   NC_002570|NP_243136.1   NC_002570|NP_241905.1   NC_002570|NP_240894.1   NC_002570|NP_241920.1   NC_002570|NP_241942.1   NC_002570|NP_241217.1   NC_002570|NP_242260.1   NC_002570|NP_240893.1   NC_002570|NP_242077.1   NC_002570|NP_241436.1   NC_002570|NP_244513.1   NC_002570|NP_241306.1   NC_002570|NP_243988.1   NC_003080|NP_203144.1   NC_006512|YP_155450.1   NC_006512|YP_155127.1   NC_006512|YP_154507.1   NC_006512|YP_154789.1   NC_006512|YP_154619.1   NC_006512|YP_156439.1   NC_006512|YP_155126.1   NC_006512|YP_155546.1   NC_006512|YP_155904.1   NC_006512|YP_154704.1   NC_006512|YP_154666.1   NC_006512|YP_154873.1   NC_006512|YP_156149.1   NC_006512|YP_155495.1   NC_006512|YP_156640.1   NC_009901|YP_001501520.1    NC_009901|YP_001503463.1    NC_009901|YP_001503247.1    NC_009901|YP_001502530.1    NC_009901|YP_001503231.1    NC_009901|YP_001503183.1NC_009901|YP_001500118.1    NC_009901|YP_001500809.1    NC_009901|YP_001503824.1    NC_009901|YP_001502529.1    NC_009901|YP_001500708.1    NC_009901|YP_001501695.1    NC_009901|YP_001504047.1NC_009901|YP_001503376.1    NC_009901|YP_001501406.1    NC_009901|YP_001500078.1    NC_009901|YP_001500551.1    NC_016147|YP_004931203.1    NC_016147|YP_004931685.1    NC_016147|YP_004930231.1NC_016147|YP_004929818.1    NC_016147|YP_004928762.1    NC_016147|YP_004931616.1    NC_016147|YP_004929081.1    NC_016147|YP_004930265.1    NC_016147|YP_004931494.1    NC_016147|YP_004928942.1NC_016147|YP_004930600.1    NC_016147|YP_004930540.1    NC_016147|YP_004928882.1    NC_016147|YP_004931319.1    NC_017248|YP_005602919.1    NC_017248|YP_005602966.1    NC_017248|YP_005603551.1NC_017248|YP_005603622.1    NC_017248|YP_005604109.1    NC_017248|YP_005604328.1    NC_017248|YP_005604706.1    NC_017248|YP_005604668.1    NC_017248|YP_005604330.1    NC_017248|YP_005604329.1NC_017248|YP_005603027.1    NC_017248|YP_005603041.1    NC_017248|YP_005604355.1    NC_017248|YP_005604414.1    NC_017248|YP_005604665.1    NC_017248|YP_005604493.1    NC_017248|YP_005602900.1NC_020238|YP_007420349.1    NC_020238|YP_007421075.1    NC_020238|YP_007420090.1    NC_020238|YP_007419317.1    NC_020238|YP_007420030.1    NC_020238|YP_007424892.1    NC_020238|YP_007423937.1NC_020238|YP_007422295.1    NC_020238|YP_007424674.1    NC_020238|YP_007419587.1    NC_020238|YP_007423552.1    NC_020238|YP_007420512.1    NC_020238|YP_007420129.1    NC_020238|YP_007421619.1NC_020238|YP_007421019.1    NC_020238|YP_007420614.1    NC_020238|YP_007423400.1    NC_020238|YP_007423686.1    NC_020238|YP_007419795.1    NC_020238|YP_007420130.1    NC_020238|YP_007419815.1NC_020238|YP_007419455.1    NC_020238|YP_007424758.1    NC_020238|YP_007420513.1    NC_020238|YP_007419247.1    NC_020238|YP_007422156.1    NC_020238|YP_007423074.1    NC_020238|YP_007419316.1NC_020238|YP_007424193.1    NC_021033|YP_007821261.1    NC_021033|YP_007821721.1    NC_021033|YP_007822326.1    NC_021033|YP_007821823.1    NC_021033|YP_007821411.1    NC_021033|YP_007821867.1NC_021033|YP_007822359.1    NC_021033|YP_007821473.1    NC_021033|YP_007821472.1    NC_021033|YP_007821938.1    NC_021033|YP_007821903.1    NC_021033|YP_007821718.1    NC_021033|YP_007822061.1NC_021033|YP_007821870.1    NC_022132|YP_008472828.1    NC_022132|YP_008473609.1    NC_022132|YP_008472967.1    NC_022132|YP_008474121.1    NC_022132|YP_008474068.1    NC_022132|YP_008473983.1NC_022132|YP_008473447.1    NC_022132|YP_008474008.1    NC_022132|YP_008473247.1    NC_022132|YP_008473161.1    NC_022132|YP_008473246.1    NC_022132|YP_008473838.1    NC_022132|YP_008474228.1NC_022132|YP_008473820.1    NC_022132|YP_008474146.1    NC_000916|NP_276806.1   NC_002570|NP_244526.1   NC_000916|NP_276784.1   NC_000916|NP_275294.1   NC_002570|NP_241030.1   NC_002570|NP_241031.1   NC_006512|YP_156785.1   NC_009901|YP_001504036.1    NC_009901|YP_001503932.1    NC_000916|NP_275838.1   NC_009901|YP_001501699.1    NC_009901|YP_001502339.1    NC_009901|YP_001504020.1    NC_000916|NP_276196.1   NC_016147|YP_004930361.1    NC_016147|YP_004928885.1    NC_017248|YP_005602814.1    NC_017248|YP_005604115.1    NC_017248|YP_005604412.1    NC_017248|YP_005604130.1    NC_020238|YP_007422466.1    NC_020238|YP_007424757.1    NC_020238|YP_007423053.1    NC_020238|YP_007422501.1    NC_020238|YP_007424454.1    NC_020238|YP_007419248.1    NC_021033|YP_007821993.1NC_002570|NP_242453.1   NC_002570|NP_241518.1   NC_002570|NP_242666.1   NC_002570|NP_241893.1   NC_002570|NP_242057.1   NC_002570|NP_241437.1   NC_002570|NP_241335.1   NC_002570|NP_244762.1   NC_002570|NP_241311.1   NC_002570|NP_241314.1   NC_002570|NP_244781.1   NC_002570|NP_241147.1   NC_002570|NP_242944.1   NC_002570|NP_241045.1   NC_002570|NP_241619.1   NC_002570|NP_242031.1   NC_002570|NP_243565.1   NC_002570|NP_243840.1   NC_002570|NP_242255.1   NC_002570|NP_241869.1   NC_002570|NP_244080.1   NC_002570|NP_244847.1   NC_002570|NP_241152.1   NC_002570|NP_241139.1   NC_002570|NP_242032.1   NC_002570|NP_244158.1   NC_002570|NP_241156.1   NC_002570|NP_243546.1   NC_002570|NP_242622.1   NC_002570|NP_243514.1   NC_002570|NP_244372.1   NC_002570|NP_241465.1   NC_002570|NP_244360.1   NC_002570|NP_244507.1   NC_002570|NP_241248.1   NC_002570|NP_241684.1   NC_002570|NP_244506.1   NC_002570|NP_242665.1   NC_002570|NP_242943.1   NC_009901|YP_001500350.1    NC_002570|NP_244541.1   NC_009901|YP_001504033.1    NC_002570|NP_243987.1   NC_016147|YP_004929013.1    NC_016147|YP_004928965.1    NC_016147|YP_004931492.1    NC_016147|YP_004930297.1    NC_017248|YP_005603335.1    NC_020238|YP_007424682.1    NC_020238|YP_007423929.1    NC_020238|YP_007424789.1    NC_020238|YP_007424238.1    NC_020238|YP_007419737.1    NC_020238|YP_007422965.1    NC_020238|YP_007420686.1    NC_020238|YP_007423624.1    NC_020238|YP_007424548.1    NC_020238|YP_007423477.1    NC_020238|YP_007424911.1    NC_020238|YP_007420302.1    NC_020238|YP_007424153.1    NC_020238|YP_007419419.1    NC_020238|YP_007422171.1NC_020238|YP_007419960.1    NC_020238|YP_007420599.1    NC_020238|YP_007422781.1    NC_020238|YP_007419982.1    NC_020238|YP_007424788.1    NC_021033|YP_007821124.1    NC_021033|YP_007821704.1NC_021033|YP_007821695.1    NC_022132|YP_008473209.1    NC_022132|YP_008472940.1    NC_022132|YP_008473367.1    NC_006512|YP_156645.1   NC_009901|YP_001503213.1    NC_020238|YP_007424863.1    NC_020238|YP_007420652.1    NC_020238|YP_007422376.1    NC_020238|YP_007422580.1    NC_021033|YP_007822031.1    NC_009901|YP_001501606.1    NC_009901|YP_001500374.1    NC_009901|YP_001503941.1NC_016147|YP_004931619.1    NC_009901|YP_001503958.1    NC_009901|YP_001503487.1    NC_009901|YP_001503590.1    NC_009901|YP_001500490.1    NC_020238|YP_007419614.1    NC_020238|YP_007423774.1NC_020238|YP_007423118.1    NC_020238|YP_007420688.1    NC_020238|YP_007422691.1    NC_016147|YP_004929180.1    NC_020238|YP_007419271.1    NC_017248|YP_005604413.1    NC_020238|YP_007421708.1NC_020238|YP_007423902.1    NC_020238|YP_007421569.1    NC_020238|YP_007419703.1    NC_020238|YP_007421870.1    NC_020238|YP_007424247.1    NC_020238|YP_007424404.1    NC_020238|YP_007422671.1NC_020238|YP_007423844.1    NC_020238|YP_007422533.1    NC_021033|YP_007821309.1
    NC_000913|NP_415787.1   NC_002570|NP_243076.1   NC_000913|NP_417319.1   NC_002570|NP_243033.1   NC_000913|NP_417378.1   NC_002570|NP_243357.1   NC_000913|NP_415026.1   NC_002570|NP_242372.1   NC_000913|NP_416921.4   NC_000913|NP_418670.1   NC_000913|NP_417476.1   NC_002570|NP_242377.1   NC_000913|NP_417036.1   NC_000913|NP_418687.1   NC_000913|NP_416136.1   NC_000913|NP_416057.1   NC_000913|NP_415128.1   NC_000913|NP_415611.1   NC_000913|NP_416641.1   NC_000913|NP_417185.1   NC_002570|NP_242416.1   NC_000913|NP_417254.4   NC_006512|YP_155429.1   NC_006512|YP_155255.1   NC_006512|YP_155729.1   NC_006512|YP_155327.1   NC_006512|YP_155181.1   NC_006512|YP_155081.1   NC_000913|NP_416123.1   NC_006512|YP_155918.1   NC_009901|YP_001501509.1    NC_009901|YP_001502003.1    NC_009901|YP_001502349.1    NC_009901|YP_001500292.1    NC_009901|YP_001501986.1    NC_009901|YP_001501933.1    NC_009901|YP_001503747.1    NC_009901|YP_001502120.1    NC_016147|YP_004931151.1    NC_016147|YP_004931013.1    NC_016147|YP_004931458.1    NC_016147|YP_004929444.1    NC_016147|YP_004930364.1    NC_016147|YP_004930559.1    NC_016147|YP_004931475.1    NC_016147|YP_004928712.1    NC_016147|YP_004928757.1    NC_016147|YP_004930325.1    NC_017248|YP_005603267.1    NC_017248|YP_005604744.1    NC_017248|YP_005604687.1    NC_017248|YP_005603278.1    NC_017248|YP_005604375.1    NC_017248|YP_005604362.1NC_017248|YP_005603504.1    NC_017248|YP_005603046.1    NC_020238|YP_007421222.1    NC_020238|YP_007424124.1    NC_020238|YP_007423535.1    NC_020238|YP_007423235.1    NC_020238|YP_007421123.1NC_020238|YP_007419985.1    NC_020238|YP_007422926.1    NC_020238|YP_007421688.1    NC_021033|YP_007821536.1    NC_021033|YP_007821016.1    NC_021033|YP_007821777.1    NC_022132|YP_008474258.1NC_022132|YP_008473927.1    NC_022132|YP_008473949.1    NC_002570|NP_242708.1   NC_002570|NP_241372.1   NC_002570|NP_242709.1   NC_002570|NP_244048.1   NC_006512|YP_154934.1   NC_002570|NP_242376.1   NC_002570|NP_243257.1   NC_002570|NP_241182.1   NC_002570|NP_241573.1   NC_002570|NP_241804.1   NC_002570|NP_244764.1   NC_002570|NP_241798.1   NC_002570|NP_241666.1   NC_002570|NP_241933.1   NC_002570|NP_243010.1   NC_016147|YP_004931673.1    NC_016147|YP_004929856.1    NC_016147|YP_004931082.1    NC_016147|YP_004930495.1    NC_016147|YP_004929610.1    NC_002570|NP_241276.1   NC_017248|YP_005603899.1    NC_017248|YP_005604104.1    NC_020238|YP_007419269.1    NC_020238|YP_007424017.1    NC_020238|YP_007422803.1    NC_020238|YP_007421962.1    NC_020238|YP_007423170.1    NC_020238|YP_007421052.1NC_020238|YP_007423374.1    NC_022132|YP_008473466.1    NC_009901|YP_001500418.1    NC_006512|YP_155874.1   NC_009901|YP_001500747.1    NC_006512|YP_155775.1   NC_009901|YP_001501955.1    NC_009901|YP_001502632.1    NC_006512|YP_156827.1   NC_006512|YP_154534.2   NC_006512|YP_154485.1   NC_006512|YP_154502.1   NC_006512|YP_154475.1   NC_006512|YP_155993.1   NC_009901|YP_001502647.1    NC_016147|YP_004931529.1    NC_016147|YP_004930815.1    NC_016147|YP_004930642.1    NC_017248|YP_005602925.1    NC_020238|YP_007423415.1    NC_020238|YP_007422305.1    NC_009901|YP_001502641.1    NC_016147|YP_004928774.1    NC_009901|YP_001502028.1    NC_016147|YP_004930367.1    NC_009901|YP_001502017.1    NC_009901|YP_001501992.1    NC_009901|YP_001502023.1    NC_009901|YP_001501969.1    NC_009901|YP_001500395.1    NC_016147|YP_004931412.1    NC_016147|YP_004930099.1    NC_016147|YP_004931667.1    NC_017248|YP_005604363.1    NC_017248|YP_005604510.1    NC_016147|YP_004930411.1NC_016147|YP_004930388.1    NC_016147|YP_004931520.1    NC_017248|YP_005603520.1    NC_020238|YP_007420644.1    NC_020238|YP_007421901.1    NC_017248|YP_005604749.1    NC_017248|YP_005604374.1NC_020238|YP_007420315.1    NC_020238|YP_007423401.1    NC_020238|YP_007422918.1    NC_020238|YP_007420064.1    NC_020238|YP_007422689.1    NC_020238|YP_007421824.1    NC_020238|YP_007421665.1
    NC_000913|NP_416477.1   NC_000916|NP_275587.1   NC_000913|NP_418536.1   NC_000913|NP_415102.1   NC_000913|NP_415513.2   NC_000913|NP_418347.1   NC_000913|NP_416723.1   NC_000913|NP_416126.1   NC_000913|NP_418431.1   NC_000913|NP_414934.1   NC_000913|NP_416582.1   NC_000913|NP_417266.1   NC_000913|YP_026207.1   NC_000913|NP_418816.1   NC_002570|NP_241239.1   NC_002570|NP_242811.1   NC_002570|NP_242786.1   NC_002570|NP_244022.1   NC_000913|NP_418305.1   NC_002570|NP_242668.1   NC_002570|NP_243129.1   NC_000913|NP_416722.2   NC_000913|NP_417498.1   NC_000913|NP_417863.1   NC_002570|NP_242413.1   NC_006512|YP_156029.1   NC_006512|YP_156814.1   NC_006512|YP_155592.1   NC_006512|YP_156491.1   NC_006512|YP_156114.1   NC_006512|YP_154713.1   NC_006512|YP_156817.1   NC_000913|NP_416871.1   NC_000913|NP_417051.2   NC_009901|YP_001503954.1    NC_009901|YP_001503779.1    NC_009901|YP_001502820.1    NC_009901|YP_001501220.1    NC_009901|YP_001500739.1    NC_009901|YP_001503863.1    NC_009901|YP_001503774.1    NC_009901|YP_001500491.1    NC_009901|YP_001500771.1    NC_015963|YP_004821697.1    NC_016147|YP_004929463.1    NC_016147|YP_004931113.1    NC_016147|YP_004930812.1    NC_016147|YP_004928847.1    NC_016147|YP_004929107.1    NC_016147|YP_004929562.1    NC_016147|YP_004930161.1    NC_016147|YP_004930186.1    NC_017248|YP_005603425.1    NC_017248|YP_005604274.1    NC_017248|YP_005603133.1NC_017248|YP_005603895.1    NC_020238|YP_007419743.1    NC_020238|YP_007419826.1    NC_020238|YP_007420786.1    NC_020238|YP_007423982.1    NC_020238|YP_007421221.1    NC_020238|YP_007420629.1NC_021033|YP_007822333.1    NC_021033|YP_007821567.1    NC_021033|YP_007822214.1    NC_022132|YP_008473871.1    NC_022132|YP_008473566.1    NC_002570|NP_244894.1   NC_009901|YP_001501042.1    NC_016147|YP_004929074.1    NC_017248|YP_005603428.1    NC_020238|YP_007421237.1    NC_000916|NP_275317.1   NC_020238|YP_007422472.1    NC_002570|NP_244292.1   NC_002570|NP_242039.1   NC_002570|NP_242254.1   NC_002570|NP_242675.1   NC_002570|NP_241685.1   NC_002570|NP_242447.1   NC_002570|NP_242879.1   NC_006512|YP_155836.1   NC_002570|NP_244344.1   NC_002570|NP_243815.1   NC_002570|NP_242020.1   NC_016147|YP_004930588.1    NC_017248|YP_005604351.1    NC_020238|YP_007422447.1    NC_020238|YP_007419413.1    NC_020238|YP_007423024.1    NC_020238|YP_007420376.1    NC_020238|YP_007424261.1    NC_020238|YP_007423930.1    NC_020238|YP_007422463.1    NC_021033|YP_007822035.1    NC_022132|YP_008473570.1    NC_022132|YP_008473326.1    NC_006512|YP_154994.1   NC_006512|YP_156768.1   NC_006512|YP_156232.1   NC_009901|YP_001503548.1    NC_006512|YP_154488.1   NC_006512|YP_156386.1   NC_016147|YP_004929745.1    NC_006512|YP_156501.1   NC_006512|YP_156041.1   NC_020238|YP_007420252.1    NC_020238|YP_007420805.1    NC_020238|YP_007424071.1    NC_006512|YP_156533.1   NC_020238|YP_007421868.1    NC_009901|YP_001501039.1    NC_009901|YP_001502374.1    NC_009901|YP_001500149.1    NC_009901|YP_001502230.1    NC_009901|YP_001501294.1    NC_009901|YP_001501944.1    NC_016147|YP_004931542.1    NC_009901|YP_001503424.1    NC_016147|YP_004929588.1    NC_009901|YP_001501613.1NC_017248|YP_005603109.1    NC_017248|YP_005604799.1    NC_009901|YP_001502892.1    NC_020238|YP_007419575.1    NC_009901|YP_001502412.1    NC_016147|YP_004930781.1    NC_016147|YP_004930045.1NC_016147|YP_004928931.1    NC_020238|YP_007424074.1    NC_016147|YP_004929598.1    NC_016147|YP_004931348.1    NC_016147|YP_004930778.1    NC_022132|YP_008474131.1    NC_020238|YP_007424980.1NC_017248|YP_005603821.1    NC_017248|YP_005603394.1    NC_017248|YP_005603151.1    NC_017248|YP_005604804.1    NC_020238|YP_007419756.1    NC_020238|YP_007419420.1    NC_020238|YP_007422557.1NC_020238|YP_007424496.1    NC_020238|YP_007422215.1    NC_020238|YP_007420664.1    NC_020238|YP_007424185.1
    NC_000913|NP_417864.1   NC_000916|NP_275590.1   NC_000913|NP_414933.1   NC_000916|NP_275588.1   NC_000913|NP_416396.1   NC_000913|NP_416478.2   NC_000913|NP_415751.1   NC_000913|NP_415648.1   NC_000913|NP_418537.1   NC_002570|NP_241238.1   NC_002570|NP_244023.1   NC_000913|NP_415222.1   NC_002570|NP_242019.1   NC_000913|NP_416583.1   NC_002570|NP_242810.1   NC_002570|NP_242446.1   NC_000913|NP_418348.1   NC_002570|NP_244895.1   NC_000913|NP_418815.1   NC_000913|NP_415103.1   NC_000913|NP_416125.2   NC_000913|NP_415515.1   NC_000913|NP_418818.1   NC_000913|NP_417497.1   NC_006512|YP_156492.1   NC_006512|YP_156030.1   NC_006512|YP_154712.1   NC_006512|YP_156042.1   NC_006512|YP_155505.1   NC_006512|YP_156815.1   NC_006512|YP_154487.1   NC_006512|YP_154883.1   NC_009901|YP_001501604.1    NC_009901|YP_001503862.1    NC_009901|YP_001502821.1    NC_009901|YP_001501241.1    NC_009901|YP_001503955.1    NC_009901|YP_001503778.1    NC_009901|YP_001503359.1    NC_009901|YP_001500740.1    NC_009901|YP_001503197.1NC_009901|YP_001500595.1    NC_015963|YP_004821696.1    NC_016147|YP_004929561.1    NC_016147|YP_004931840.1    NC_016147|YP_004928846.1    NC_016147|YP_004929764.1    NC_016147|YP_004930185.1NC_016147|YP_004929462.1    NC_016147|YP_004930128.1    NC_016147|YP_004931112.1    NC_016147|YP_004930813.1    NC_017248|YP_005603416.1    NC_017248|YP_005604273.1    NC_017248|YP_005604848.1NC_017248|YP_005604798.1    NC_017248|YP_005603424.1    NC_020238|YP_007422448.1    NC_020238|YP_007419421.1    NC_020238|YP_007420628.1    NC_020238|YP_007424981.1    NC_020238|YP_007422974.1NC_020238|YP_007423931.1    NC_020238|YP_007419742.1    NC_021033|YP_007821503.1    NC_021033|YP_007822334.1    NC_021033|YP_007821568.1    NC_022132|YP_008473565.1    NC_022132|YP_008473850.1NC_022132|YP_008474130.1    NC_000916|NP_275583.1   NC_000916|NP_276719.1   NC_000916|NP_276038.1   NC_000916|NP_275691.1   NC_000916|NP_276039.1   NC_009901|YP_001500416.1    NC_009901|YP_001502232.1    NC_000916|NP_276870.1   NC_000916|NP_275600.1   NC_016147|YP_004930279.1    NC_016147|YP_004928930.1    NC_016147|YP_004929075.1    NC_020238|YP_007419827.1    NC_020238|YP_007424243.1    NC_002570|NP_241686.1   NC_002570|NP_242776.1   NC_002570|NP_243099.1   NC_002570|NP_244779.1   NC_002570|NP_243130.1   NC_002570|NP_241154.1   NC_002570|NP_242038.1   NC_002570|NP_241621.1   NC_002570|NP_244293.1   NC_002570|NP_241137.1   NC_002570|NP_243567.1   NC_002570|NP_242674.1   NC_009901|YP_001503476.1    NC_002570|NP_241392.1   NC_009901|YP_001501292.1    NC_002570|NP_244661.1   NC_009901|YP_001503928.1    NC_002570|NP_240874.1   NC_016147|YP_004930589.1    NC_017248|YP_005604344.1    NC_017248|YP_005602945.1    NC_020238|YP_007423846.1    NC_020238|YP_007422507.1    NC_020238|YP_007420250.1    NC_020238|YP_007420804.1    NC_020238|YP_007420378.1    NC_020238|YP_007419412.1    NC_020238|YP_007423983.1    NC_020238|YP_007424262.1    NC_006512|YP_154558.1   NC_006512|YP_155485.1   NC_009901|YP_001501253.1    NC_006512|YP_155597.1   NC_009901|YP_001500492.1    NC_006512|YP_156095.1   NC_020238|YP_007424223.1    NC_020238|YP_007422379.1    NC_020238|YP_007422214.1NC_020238|YP_007421220.1    NC_009901|YP_001502787.1    NC_009901|YP_001502373.1    NC_009901|YP_001500198.1    NC_009901|YP_001502663.1    NC_009901|YP_001502091.1    NC_009901|YP_001503425.1NC_009901|YP_001503449.1    NC_009901|YP_001500165.1    NC_020238|YP_007419757.1    NC_022132|YP_008472776.1    NC_016147|YP_004931541.1    NC_016147|YP_004930044.1    NC_016147|YP_004929587.1NC_016147|YP_004928825.1    NC_017248|YP_005604712.1    NC_020238|YP_007421867.1    NC_020238|YP_007424495.1    NC_020238|YP_007421236.1    NC_020238|YP_007424764.1    NC_020238|YP_007424552.1NC_020238|YP_007424070.1    NC_020238|YP_007422555.1    NC_022132|YP_008473569.1
    NC_000913|NP_416724.1   NC_002570|NP_243814.1   NC_000913|NP_417880.1   NC_002570|NP_241403.1   NC_000913|NP_417049.1   NC_000913|NP_417211.1   NC_000913|NP_415839.1   NC_002570|NP_242745.1   NC_000913|NP_414864.1   NC_000913|NP_417189.2   NC_000913|NP_417345.1   NC_002570|NP_241858.1   NC_000913|NP_416986.4   NC_002570|NP_244767.1   NC_000913|NP_415819.4   NC_000913|NP_418432.1   NC_000913|NP_418304.1   NC_000913|NP_415153.1   NC_006512|YP_156963.1   NC_006512|YP_156816.1   NC_000913|NP_417727.1   NC_006512|YP_156670.1   NC_006512|YP_155593.1   NC_006512|YP_155113.1   NC_006512|YP_154588.1   NC_006512|YP_155797.1   NC_006512|YP_155122.1   NC_000913|NP_415719.2   NC_009901|YP_001501295.1    NC_009901|YP_001501614.1    NC_009901|YP_001500252.1    NC_009901|YP_001503170.1    NC_009901|YP_001501310.1    NC_009901|YP_001502525.1    NC_016147|YP_004929744.1    NC_016147|YP_004931524.1    NC_016147|YP_004929108.1    NC_016147|YP_004929327.1    NC_016147|YP_004931622.1    NC_017248|YP_005603894.1NC_020238|YP_007419730.1    NC_020238|YP_007422240.1    NC_020238|YP_007419468.1    NC_020238|YP_007422327.1    NC_020238|YP_007420168.1    NC_021033|YP_007821613.1    NC_021033|YP_007821101.1NC_022132|YP_008473759.1    NC_000916|NP_275692.1   NC_002570|NP_243834.1   NC_002570|NP_243632.1   NC_002570|NP_244654.1   NC_006512|YP_155591.1   NC_002570|NP_244812.1   NC_002570|NP_244705.1   NC_009901|YP_001501219.1    NC_009901|YP_001499949.1    NC_002570|NP_242692.1   NC_002570|NP_243605.1   NC_009901|YP_001503938.1    NC_009901|YP_001501221.1    NC_016147|YP_004929023.1    NC_017248|YP_005603892.1NC_020238|YP_007424841.1    NC_006512|YP_156531.1   NC_006512|YP_156442.1   NC_009901|YP_001503210.1    NC_006512|YP_154927.1   NC_009901|YP_001503292.1    NC_016147|YP_004929583.1    NC_020238|YP_007421638.1    NC_009901|YP_001503216.1    NC_009901|YP_001501634.1    NC_009901|YP_001503775.1    NC_009901|YP_001500582.1    NC_009901|YP_001501943.1    NC_020238|YP_007419660.1    NC_020238|YP_007423568.1    NC_021033|YP_007822213.1    NC_016147|YP_004931436.1
    
  2. Paralogs

    NC_020238|YP_007420194.1    NC_020238|YP_007420199.1    NC_020238|YP_007421388.1    NC_020238|YP_007422556.1    NC_020238|YP_007421295.1    NC_020238|YP_007422519.1    NC_020238|YP_007422868.1    NC_020238|YP_007419313.1    NC_020238|YP_007422870.1    NC_020238|YP_007423429.1    NC_020238|YP_007424554.1    NC_020238|YP_007419582.1    NC_020238|YP_007424027.1    NC_020238|YP_007421297.1    NC_020238|YP_007424852.1    NC_020238|YP_007419896.1    NC_020238|YP_007421517.1    NC_020238|YP_007424277.1    NC_020238|YP_007419311.1    NC_020238|YP_007422308.1    NC_020238|YP_007424965.1    NC_020238|YP_007424556.1    NC_020238|YP_007420196.1    NC_020238|YP_007423077.1    NC_020238|YP_007419782.1    NC_020238|YP_007424967.1    NC_020238|YP_007422134.1    NC_020238|YP_007422606.1    NC_020238|YP_007421515.1    NC_020238|YP_007424854.1    NC_020238|YP_007422892.1    NC_020238|YP_007424026.1    NC_020238|YP_007420846.1    NC_020238|YP_007421386.1    NC_020238|YP_007422608.1    NC_020238|YP_007419894.1    NC_020238|YP_007419780.1
    NC_002570|NP_244374.1   NC_002570|NP_243243.1   NC_002570|NP_242247.1   NC_002570|NP_243020.1   NC_002570|NP_242567.1   NC_002570|NP_242552.1   NC_002570|NP_241820.1   NC_002570|NP_244452.1   NC_002570|NP_242339.1   NC_002570|NP_243788.1   NC_002570|NP_243343.1   NC_002570|NP_242204.1   NC_002570|NP_243507.1   NC_002570|NP_243844.1   NC_002570|NP_244275.1   NC_002570|NP_242049.1   NC_002570|NP_242829.1   NC_002570|NP_243517.1   NC_002570|NP_243070.1   NC_002570|NP_244113.1   NC_002570|NP_243338.1   NC_002570|NP_244432.1
    NC_009901|YP_001501354.1    NC_009901|YP_001501833.1    NC_009901|YP_001500880.1    NC_009901|YP_001499887.1    NC_009901|YP_001503552.1    NC_009901|YP_001500436.1    NC_009901|YP_001500544.1    NC_009901|YP_001502124.1    NC_009901|YP_001503914.1    NC_009901|YP_001500967.1    NC_009901|YP_001501483.1    NC_009901|YP_001500660.1    NC_009901|YP_001502935.1    NC_009901|YP_001499880.1    NC_009901|YP_001503109.1    NC_009901|YP_001502279.1    NC_009901|YP_001501475.1    NC_009901|YP_001500265.1    NC_009901|YP_001502320.1    NC_009901|YP_001502427.1    NC_009901|YP_001501772.1    NC_009901|YP_001502186.1
    NC_002570|NP_242278.1   NC_002570|NP_242213.1   NC_002570|NP_240989.1   NC_002570|NP_244003.1   NC_002570|NP_240955.1   NC_002570|NP_242812.1   NC_002570|NP_244366.1   NC_002570|NP_243640.1   NC_002570|NP_244619.1   NC_002570|NP_241534.1   NC_002570|NP_242036.1   NC_002570|NP_243833.1   NC_002570|NP_241136.1   NC_002570|NP_242795.1   NC_002570|NP_241633.1   NC_002570|NP_241282.1   NC_002570|NP_242173.1   NC_002570|NP_241111.1   NC_002570|NP_241245.1   NC_002570|NP_241915.1   NC_002570|NP_242412.1
    NC_000916|NP_275317.1   NC_000916|NP_276388.1   NC_000916|NP_275266.1   NC_000916|NP_276120.1   NC_000916|NP_275589.1   NC_000916|NP_276039.1   NC_000916|NP_275762.1   NC_000916|NP_275602.1   NC_000916|NP_276038.1   NC_000916|NP_276252.1   NC_000916|NP_275499.1   NC_000916|NP_275927.1   NC_000916|NP_275962.1   NC_000916|NP_275611.1   NC_000916|NP_275503.1   NC_000916|NP_275435.1
    

How can I visualise the Ortholog and Paralog genes?

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9
  • $\begingroup$ One tree for each, network phylogeny for paralogs $\endgroup$
    – M__
    May 24 '19 at 18:44
  • $\begingroup$ The third solution is a Chord diagram ... which is what circos looks like $\endgroup$
    – M__
    May 24 '19 at 20:00
  • $\begingroup$ Are there any examples of how to convert the output from PorthoMCL into any of the above 3 solutions? $\endgroup$
    – user977828
    May 28 '19 at 5:53
  • $\begingroup$ I'll put together a network tree, then post it back here. It will be a while before I get chance to do this though $\endgroup$
    – M__
    May 28 '19 at 12:41
  • $\begingroup$ I just hope you are not in a hurry, I'll use this data set on the single line starting NC_020238|YP_007420194.1 and ending NC_020238|YP_007419780.1 and see what I get. $\endgroup$
    – M__
    May 28 '19 at 12:55

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