[Bioperl-l] seqboot and random seeds
junet9876 at yahoo.com
Mon Jun 14 00:33:10 EDT 2004
I was just wondering if someone could please tell me
how random seeds are handled in the SeqBoot module.
For example, is there a way to find out what random
number is being used, is it the same each time?
--- Joe Felsenstein <joe at gs.washington.edu> wrote:
> Date: Sun, 13 Jun 2004 08:38:09 -0700
> From: Joe Felsenstein <joe at gs.washington.edu>
> To: june tantoolvesm <junet9876 at yahoo.com>
> Subject: Re: bootstrapping related question
> June Tantoolvesm --
> > I have automated a few of your programs into a
> > pipeline using bioperl
> > (seqboot->protdist->neighbor->consense). My
> > is, the final trees I get from when I run the
> > manually and from when I use bioperl, are not the
> > same. I tried several times.
> > Is it normal to not get the same tree everytime we
> > the pipeline of programs
> > (seqboot->protdist->neighbor->consense). (But
> > I do get the same tree when I run the programs
> > manually a few times, so I'm confused.) Also, does
> > this have anything to do with the random seed
> > we input for seqboot?
> You should get the same tree each time when you run
> Bioperl script, provided that it properly renames
> and provided that the random number seeds used are
> same each time. There is no reason to expect them
> be different.
> Check on the issue of random number seeds, and
> whether the
> output files have been renamed to input files
> Joe Felsenstein joe at gs.washington.edu
> Department of Genome Sciences and Department of
> University of Washington, Box 357730, Seattle, WA
> 98195-7730 USA
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