Thank you for your reply.
> Might also be useful to look at some of the functions in seqinR.
> Sorry about this, but can I ask an off topic question? Many
> alignment algorithms are available. Are we replicating the effort of
> programs like Bioperl/EMBOSS etc etc in R? What are people's
> with RSperl and other "connectivity" modules?
There are some algorithm which was originally implemented in other
environment, but has been re-written in R later due to the popularity
the usage of R.
In stead of spending time learning (there is still a decent percentage
R users that don't know Perl well), I think maybe most user prefer to
it written in R, even an less perfect version. One can always go to
better-written algorithm later if there is a need.
Well, this is just my personal opinion.
Fangxin Hong Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
(Phone): 858-453-4100 ext 1105