Phylogeny on 1800 protein sequences (alignment length 1500 characters)

[Daniel John Rigden]

Hi Michael

This new program might help

http://bioinformatics.oupjournals.org/cgi/content/abstract/18/11/1546

good luck

Dan

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On Tue, 10 Dec 2002, Michael Spitzer wrote:

> Hi!
>
> I'm about to infer a tree on approx. 1800 aligned protein sequences,
> with the lengt of the alignment being approx. 1500 characters.
> I would like to ask here what kind of programs /algorithms are there
> to get the tree as fast as possible.
> Right now I'm using CLUSTALW's neighbor-joining with 100 bootstrap
> trials.
> The alignment procedure took ~18 hours on my 1,4GHz P3, but the
> NJ/bootstrapping wasn't finished after ~5 days (job killed due to
> power loss, it's my private PC...).
>
> Are there any other NJ-implementations out there which are faster than
> CLUSTAW and/or use parallelism (we have a 20 node SUN cluster (mixed
> 350 and 450 MHz CPUs...) at work, which (per node) is quite slow
> compared to my 1,4Ghz P3, but utilizing more nodes could speed things
> up)?
> I tried PARBOOT (uses PHYLIP programs), but PHYLIP turned out to be a
> lot slower than CLUSTALW (in fact the distance matrix calculation
> step. A single CPU CLUSTALW job is nearly 20 times faster than ~20
> node PARBOOT job on our cluster).
>
> Thanks in advance,
>
> Michael
>
>