[R] Clustalw again

Wolski wolski at molgen.mpg.de
Mon Jun 14 19:46:17 CEST 2004

Hi Daniela!

I understand it right? You want to compute an multiple alignment of 37000 sequences at once?
There are no multiple alignment programs in the world that can compute a multiple alignment of 37000 sequences to my knowledge.
Sincerely Eryk.

What you can try is to cluster the sequences according their pairwise sequence alignment and compute multiple alignments for similar sequences.
But you will need a fast algorithm like BLAST algorithm and this on to  on is not implemented in R.

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On 14.06.2004 at 17:39 daniela.marconi at libero.it wrote:

>I try to have again some tips about clustalw function  (in dna package).
>I try to use this function on a windos platform, but my pc doesn`t have
>enough memory(512 Mb) for allocation, analizing a file with more or less
>37250 sequences , so i try on a linux platform and every time i have a
>segmentation fault!!
>What is the problem?Do you think that also on linux platform memory is the
>problem (1Gb)?
>Thanks agin
>R-help at stat.math.ethz.ch mailing list
>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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