Hello David, Mike and Thomas

Dear David,
First, my apologies for the double posting - I'll try to not forget that
policy.
Regarding agrep, I think it will be easier for me to work with the functions
on {Biostrings} (for example stringDist, or pairwiseAlignment), then to open
up the C code.


Dear Mike and Thomas,

>From what I gathered here (Thanks to Joris Meys):
http://stackoverflow.com/questions/4497747/how-to-perform-basic-multiple-sequence-alignments-in-r/4498434#4498434
There is an R interface to the MUSCLE algorithm in the bio3d package
(function seqaln()).
But not one for clustal.

I will probably end up using pairwiseAlignment on pairs of allignments with
some sort of stopping rules (I'll have to play with it to see how it works).

Thank you all for your answers.
It is always helpful to from others if something was already implemented in
R or not.

Best,
Tal


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On Tue, Dec 21, 2010 at 2:44 PM, Mike Marchywka <marchywka@hotmail.com>wrote:

> e came
> here with a task and was pointed to bio packages but I
> thought there m
>

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