Hi,

I've been using the DNAbin class and the dist.dna() function in a package I've been making to get a matrix of hamming distances between DNA sequences in a multiple sequence alignment. I've done this with sequences hundreds of thousands long but want to allow the capability to use sequences from genome data i.e. Mbp long. I know there is a Biostring package in the Bioconductor project that is supposed to store very big sequences effectively. Can I do an equivalent job with Bio-strings yielding me such distance information, and can I also identify all the SNPs in an alignment with these large sequences i.e. the segregating sites? If so how?

Many Thanks,
Ben.



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