bootstrap analysis

manishbudathoki

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Join Date: Oct 2010

Posts: 4
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#1

bootstrap analysis

11-02-2010, 06:00 AM

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
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andreas.sjodin

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Join Date: Apr 2009

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#2

11-02-2010, 08:09 AM

You may use MEGA for this kind of analysis.
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epigen

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Join Date: May 2010

Posts: 101
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#3

11-02-2010, 08:46 AM

Another possibility is PHYLIP:

Felsenstein/Kuhner lab

http://evolution.genetics.washington.edu/phylip.html
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