sequence similarity in R

Question

[kng]

I use emboss water on the command line to do pairwise sequence alignment. It worked fine for a few sequences, but I now have a list of 100s of sequences to check pairwise alignment for. Is there a way to automate this in R ?

[Joe]

You can shell-out from R as you can with most languages, but I'd question using R for this really. If you've already done alignments on the commandline, stay on the commandline.

All you need is a shell loop or some GNU parallel usage to achieve this. It can even be done as a one-line shell command.