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janaki at cdacindia.com janaki at cdacindia.com
Tue Dec 10 21:32:56 EST 2002


Hi,
I think you can try parallel version of TRee-Puzzle..
http://www.tree-puzzle.de/
Check it out...may be useful..
Regards
Janaki


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
> 




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