clustalW
2
0
Entering edit mode
John Lande ▴ 280
@john-lande-2357
Last seen 7.9 years ago
dear all, is there a an implementation of clustalw in bioconductor? -- John [[alternative HTML version deleted]]
• 809 views
ADD COMMENT
0
Entering edit mode
@kasper-daniel-hansen-2979
Last seen 13 months ago
United States
Pairwise alignment is implemented in pairwiseALignment from Biostrings. There is not - as far as I know - any multiple alignment capabilities. But I could be wrong, there are many packages out there. Kasper On Nov 20, 2009, at 0:52 , John Lande wrote: > dear all, > > is there a an implementation of clustalw in bioconductor? > > > -- > John > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENT
0
Entering edit mode
@michael-lawrence-2759
Last seen 7.9 years ago
On Fri, Nov 20, 2009 at 12:52 AM, John Lande <john.lande77@gmail.com> wrote: > dear all, > > is there a an implementation of clustalw in bioconductor? > > > No, but I've had success with running clustalw via system(), configuring it to use fasta for input and output. > -- > John > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENT
0
Entering edit mode
Here are a few simple examples for handling and manipulating multiple and pairwise sequence alignments using Biostring's XStringSet class: http://htseq.ucr.edu/#MultipleSequenceAlignments.28MSAs.29 Thomas On Fri, Nov 20, 2009 at 06:53:26AM -0800, Michael Lawrence wrote: > On Fri, Nov 20, 2009 at 12:52 AM, John Lande <john.lande77 at="" gmail.com=""> wrote: > > > dear all, > > > > is there a an implementation of clustalw in bioconductor? > > > > > > > No, but I've had success with running clustalw via system(), configuring it > to use fasta for input and output. > > > > -- > > John > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY

Login before adding your answer.

Traffic: 389 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6