[Molecular-evolution] Re: BOOTSTRAP
(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
More information about the Mol-evol