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[Molecular-evolution] Re: BOOTSTRAP

Joe Felsenstein via mol-evol%40net.bio.net (by joe At removethispart.gs.washington.edu)
Fri Dec 1 01:08:40 EST 2006

In article <mailman.180.1164721659.19683.mol-evol At net.bio.net>,
Kira <kiyaiz At yahoo.com> wrote:
>Hello, I want to do bootstrap with Phylip (seqboot) but I have only a
>binary data or a distance matrix and I don't know how to do the
>bootstrap. Someone can help me please?

For discrete character data (binary data), use program Seqboot, with
the D option set to Discrete, then rename the outfile to infile,
then run a program that infers phylogenies from discrete data.
Use the M (multiple data set option for that program).  Then take the
outtree file, call it intree, and run Consense.

Read more about it in the documentation files  seqboot.html  and

For a distance matrix you have to bootstrap the original sequences from
which the distance was computed, and make distances for each bootstrap

I will not explain further.  I have 20,000 registered users, and
individual tutorials are too time-consuming.  Read The (documentation)
Files Meticulously (RTFM).

Joe Felsenstein         joe At removethispart.gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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