HELP: Parallel Algorithms for Phylogeny Inference

Tim Littlejohn tim at megasun.BCH.UMontreal.CA
Sat Nov 19 08:52:13 EST 1994


Todd,

In article <1994Nov16.031730.10985 at sol.UVic.CA> harold at sanjuan.UVic.CA (Todd Wareham) writes:
>I am interested in parallel algorithms for inferring phylogenetic
>trees, as well as (publicly) available/accessible implementations of
>such algorithms, e.g. e-mail servers. Might anyone who has information
>on these topics please drop me aline or post details here? Thanks in
>adavnce,

While it may not exactly be what you are looking for, we developed a method
for parallelising the bootstrapping component of various programs in the
Phylip package, which we have called parboot.  I posted an announcement about
this some time ago, but here is the URL for the package, including
documentation, etc:

URL: gopher://megasun.bch.umontreal.ca:70/11/CMB/Phylogeny/Parboot

(also available by ftp to the same site).

In brief:

PARBOOT is a parallel implementation of the bootstrapping function 
available in many of the PHYLIP(1) phylogenetic analysis programs.
The programs in the PHYLIP package that support bootstrapping take
input files with multiple resampled data sets that could potentially
be processed independently (usually generated with the PHYLIP program
SEQBOOT).  Bootstrapping is traditionally performed using the PHYLIP
programs, however, so that the constituent programs of a bootstrap
process these blocks sequentially.  This is usually a time consuming
process, making analysis through the iterative bootstrapping method
impractical.

I hope this helps,

Tim

-- 
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Tim Littlejohn

E-mail:     tim at bch.umontreal.ca  

Snail Mail: Departement de biochimie        Phone: (514) 343-6111, x5149
            Universite de Montreal          Fax:   (514) 343-2210 
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