[Bioperl-l] protal2dna and Bio::SimpleAlign

[Marc Logghe]

> yep - except you aren't required to have sequences in the 
> same order - 
> but require the sequence names to be the same in both (or you do the 
> mapping of names up-front in the hash you give to the 
> routine).
Hope people don't mind going a little off topic here ;-)
The order used to be a problem because most multiple alignment applications, like clustalw, don't preserve the order of the aligned sequences. However, this is possible now by the more recent version of clustalw where you can pass the option -outorder=input.
Peter Rice learned me how to cheat emboss' emma:
setenv EMBOSS_CLUSTALW "clustalw -outorder=input"

Marc