[BiO BB] Need fair alignment tool comparison/ using DSCAM for tool testing

Mike Marchywka marchywka at hotmail.com
Wed Feb 20 07:39:14 EST 2008

Thanks. Do you know off hand if this has a memory saving mode? It wasn't immediately obvious
from the ./mafft --help

Also, there may be some ability to use concepts from here if you want to optimize this :http://www.fftw.org/ 

I tried it on the e coli strains and the memory usage went to 1Gb ( VM limit, I only have 256M physical)
and of course ( well, doesn't have to do but normally does ) CPU went to low levels ( more VM action
than computation presumably). It seemed to know it should go to something called "memsave mode" but I'm
not sure it realized it was playing with virtaul memory ( do you know if it is supposed to
be cache aware or otherwise know about memory?): 

$ ./mafft --retree 1 /cygdrive/e/new/temp/both_fasta> xxxxx
generating 200PAM scoring matrix for nucleotides ... done
scoremtx = -1
Gap Penalty = -1.53, +0.00, -0.12

Making a distance matrix ..
    1 / 2

Constructing a UPGMA tree ...
    0 / 2

Progressive alignment ...
STEP     1 / 1
len1=4979619, len2=4639675, Switching to the memsave mode
fm FFT ...

Mike Marchywka
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> From: Sterten at aol.com
> Date: Tue, 19 Feb 2008 11:11:38 -0500
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Need fair alignment tool comparison/ using DSCAM for tool testing
> I recommend this for alignment:
> _http://align.bmr.kyushu-u.ac.jp/mafft/online/server/_
> (http://align.bmr.kyushu-u.ac.jp/mafft/online/server/)
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb

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