clustalW

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John Lande ▴ 280

@john-lande-2357

Last seen 10.3 years ago

dear all, is there a an implementation of clustalw in bioconductor? -- John [[alternative HTML version deleted]]

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ADD COMMENT • link updated 15.1 years ago by Michael Lawrence ▴ 620 • written 15.1 years ago by John Lande ▴ 280

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Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 18 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 • link 15.1 years ago Kasper Daniel Hansen ★ 6.5k

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Michael Lawrence ▴ 620

@michael-lawrence-2759

Last seen 10.3 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 • link 15.1 years ago Michael Lawrence ▴ 620

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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 • link 15.1 years ago Thomas Girke ★ 1.7k

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