[Jalview-discuss] pairwise alignement does not work on DNA

[Jim Procter]

barry kesner wrote:
>    The latest download of Jalview does not pairwise align DNA for me.   
> Does anyone have a problem with this?
> I would like it to global align pairs of DNA sequences?
>   
Hello Barry.

It sounds like you have some non-nucleotide symbols (or 'X's) in your 
sequences, these cause an exception in the pairwise alignment routine. 
The work around is to use the find function in your seuqences to find 
the non nucleotide characters, and use the edit sequence function to 
change them to proper nucleotide.

A bug fix will be made in the future which will handle this problem more 
effectively, but for now - this is the best I can do.

Jim.