Try GeneDoc, it accepts both and will do exactly what you need.
Virpi Ahola wrote:
> I've done a multiple sequence alignment to the protein sequences. In
> addition, I've a secondary structure assignments for each sequence
> derived from DSSP. Does anybody know a software that combines these two
> files so that the different seconary structure periods would be marked
> with the different colour in the multiple alignment ?
>> Thanks for all tips,