John Calley <jnc at becker.biosci.arizona.edu> writes:
> Ideally I'd like to have a program take both
>secondary structure and primary structure into consideration in doing an
>alignment but I'd settle for just secondary structure. Does anyone
>have any suggesions?
xalign (from ftp://canopus.biochem.ualberta.ca/pub/) allows you to
use secondary structure information for all sequences, and will use
bith primary and secondary structure information for the alignment.
It also allows you to "anchor" sequences at positions were you are
certain that they should be aligned.
Cheers,
Martin
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