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Dear Nora, Package ape from CRAN offers functions for this type of an analysis. Use dist.dna to calculate pairwise distances, and then make a neighbor- joining tree using the function nj. This gives you the initial tree. You can then perform bootstrapping analysis, and calculate a consensus of the trees calculated from these bootstrapped replicates (check the ape help for this). This stage is rather slow in ape, and I typically use external software such as PHYLIP package (use Google to find it) for this, or even for the whole analysis. Best Regards, Jarno On Sun, 4 Mar 2007, Nora Muda wrote: > Dear Bioconductor useRs, > > I have 30 aligned DNA sequences and want to resample it with > replacement based on the positions of the sequences to create resampled > data sets with the same size of sequences. Does anyone know which > packages are supported and suitable to use? > > From the resampled data sets then I have to compute the pairwise > distances with using say, Kimura's 2 parameter to construct phylogenetic > tree. Is there any suitable packages that I can use? > > Thank you in advance for any help. > > > Regards, > Nora. > > > > ____________________________________________________________________ ________________ > Bored stiff? Loosen up... > > > [[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 > ---------------------------------------------------------------------- ------- Jarno Tuimala, FT, bioinformatiikan asiantuntija, CSC, PL 405, 02101 Espoo puh.: (09) 457 2226, fax: (09) 457 2302, s-posti: jarno.tuimala at csc.fi CSC on tieteen tietotekniikan keskus, http://www.csc.fi/molbio Jarno Tuimala, PhD, bioinformatics, CSC, P.O.Box 405, FI-02101 Espoo, Finland tel.: +358 9 457 2226, fax: +358 9 457 2302, e-mail: jarno.tuimala at csc.fi CSC is the Finnish IT Center for Science, http://www.csc.fi/molbio

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