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 reallocating... done. reallocating... done. generating 200PAM scoring matrix for nucleotides ... done scoremtx = -1 Gap Penalty = -1.53, +0.00, -0.12 Making a distance matrix .. 1 / 2 done. Constructing a UPGMA tree ... 0 / 2 done. Progressive alignment ... STEP 1 / 1 len1=4979619, len2=4639675, Switching to the memsave mode fm FFT ... Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only [EMAIL PROTECTED] Note: Hotmail is blocking my mom's entire ISP claiming it is to reduce spam but probably to force users to use hotmail. Please DON'T assume I am ignoring you and try me on [EMAIL PROTECTED] if no reply here. Thanks. > From: [EMAIL PROTECTED] > Date: Tue, 19 Feb 2008 11:11:38 -0500 > To: [email protected] > 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 > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Climb to the top of the charts! Play the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
