Question: clustalW
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gravatar for John Lande
10.1 years ago by
John Lande280
John Lande280 wrote:
dear all, is there a an implementation of clustalw in bioconductor? -- John [[alternative HTML version deleted]]
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ADD COMMENTlink modified 10.1 years ago by Michael Lawrence620 • written 10.1 years ago by John Lande280
Answer: clustalW
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gravatar for Kasper Daniel Hansen
10.1 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
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 COMMENTlink written 10.1 years ago by Kasper Daniel Hansen6.4k
Answer: clustalW
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gravatar for Michael Lawrence
10.1 years ago by
Michael Lawrence620 wrote:
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 COMMENTlink written 10.1 years ago by Michael Lawrence620
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 REPLYlink written 10.1 years ago by Thomas Girke1.7k
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