Support for nexus in alignment format

[Peter Rice]

Henrikki Almusa wrote:
> I read through the alignment formats that emboss supports. I was wondering if 
> nexus is supported as alignment format (-aformat nexus)? I seems to be 
> supported as sequence format but it wasnt mentioned as alignment format.

The sequence formats are easy to add as alignment formats. Not sure 
quite how useful that is.

You can do this:

1. Create your alignment in a sequence format (FASTA, MSF)

2. Use seqret to convert to nexus format

... or does NEXUS format hold some extra information that would make it 
a useful alignment format, and that we lose by going through FASTA?

Hope this helps,

Peter