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  • manishbudathoki
    Junior Member
    • Oct 2010
    • 4
    #1

    bootstrap analysis

    can anyone tell me how to do bootstrap analysis for homologous protein sequence? and how to use NJ plot to visualize branch lenght and bootstrap values?
    This below are the protein sequences result that i have to do bootstrap analysis.

    >Mb_Gg
    MGLSDQEWQQVLTIWGKVEADIAGHGHEVLMRLFHDHPETLDRFDKFKGLKTPDQMKGSEDLKKHGATVL
    TQLGKILKQKGNHESELKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHAADFGADSQAAMKKALELFR
    NDMASKYKEFGFQG


    >Mb_Tg
    MGLSDQEWQQVLTVWGKVESDLAGHGHQILMRLFQDHPETLDRFEKFKGLKTPDAMKGSEDLKKHGVTVL
    TQLGKILKAKGNHEAELKPLAQTHATKHKIPVKYLEFISEVIIKVLAEKHAADFGADAQAAMKKALELFR
    NDMATKYKEFGFQG


    >Mb_Af
    MGLNDQEWQQVLTMWGKVESDLAGHGHAVLMRLFQDHPETMDRFDKFRGLKTPDQMRGSEDMKKHGVTVL
    TQLGKILKQKGHHESELKPLAQTHATKHRVPVKYLEFICEAIMKVIAEKHSADFGANCQAAMKKALELFR
    HDMASRYKEFGFQG


    >Mb_Cf
    MGLSDGEWQLVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSEDLKKHGNTVL
    TALGGILKKKGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQSKHSGDFHADTEAAMKKALELFR
    NDIAAKYKELGFQG


    >Mb_Hs
    MELGCQVCKYCAMGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKA
    SEDLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADA
    QGAMNKALELFRKDMASNYKELGFQG
    Tags: None
    • andreas.sjodin
      Member
      • Apr 2009
      • 27
      #2
      You may use MEGA for this kind of analysis.

        Comment

        • epigen
          Senior Member
          • May 2010
          • 101
          #3
          Another possibility is PHYLIP:
          Felsenstein/Kuhner lab
          http://evolution.genetics.washington.edu/phylip.html

            Comment

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