[BioC] resample of DNA/protein sequences and compute pairwise distances

[Jarno Tuimala]

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.
>
>
>
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-----------------------------------------------------------------------------
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