R package for sequence homology

Question

[floris.barthel]

I'm looking for an R package that can calculate sequence homology between two sequences, identical to what this online program does: http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=shuffle

I've been searching around but havent had any luck. Can anyone give any pointers?

[poisonAlien]

Have you already looked at biostrings ? (May be not exactly same as shuffle)