Hi Fabricia, I have a package in development on github ( https://github.com/fmichonneau/seqManagement) that happens to include a function that does what you are looking for: it splits this kind of files to produce one file per alignment. You want to look at the function called splitMultiAlignments.
Don't hesitate to let me know if you need help to make it run. Cheers, -- François On Thu, Mar 13, 2014 at 12:56 PM, Fabricia Nascimento < nasciment...@yahoo.com.br> wrote: > > Hi, > > I am new to R and I am > trying to read a file containing sets of multiple sequence alignments as in > the example below. The difference is that for my files, each set of > sequences > may contain up to 50 sequences of 10,000bp each. > > > Example: > > 5 10 > Seq0 ATCGTTATTA > Seq1 AGCGTTATTA > Seq15 ATCCTTATTA > Seq20 ATCGATATTA > Seq30 ATCGTAATTA > 5 10 > Seq1 ATCGTTATTA > Seq2 ATCGTTATTA > Seq4 ATCCTTATTA > Seq5 ATCGTTGTTA > Seq7 ATCGTTACCA > 5 10 > Seq1 ATCGTTATTA > Seq2 ATTGTTATTA > Seq4 ATCGTTATTA > Seq19 AACGTTATTA > Seq2 ATCGAAATTA > > > I did try to use read.dna > from the ape package. Although it seems to read the whole file, I donât > know > how to access the individual multiple alignments and create a NJ tree for > each > of these alignments. > > I would appreciate very much > if someone knows of any function that can do that. Or whether I will need > to > pre-process my files first. > I will need to create a NJ > tree for each set of alignment and then I will use the apTreeshape package > in R > to calculate index for tree shape. > > Thanks very much in advance! > Fabricia. > [[alternative HTML version deleted]] > > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > [[alternative HTML version deleted]]
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