[Molecular-evolution] Re: BOOTSTRAP

kira via mol-evol%40net.bio.net (by kiyaiz At yahoo.com)
Sun Dec 3 04:56:04 EST 2006


Thank you very much, I did it. I read the documentation file but my
english is not very good and I can't  undertand all, so  I always did
something wrong, the problem was whith M but now I did it so thanks for
your explain, it help me a lot.


Joe Felsenstein ha scritto:

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