[Biopython-dev] Questions about the NEXUS format

[Peter]

Hello again Frank,

As Biopython's NEXUS expect, I've got a couple of hopefully trivial
questions about the format, which connect to how best to handle it the
Bio.SeqIO and Bio.AlignIO modules.  http://biopython.org/wiki/SeqIO
http://biopython.org/wiki/AlignIO

My short questions are:

Q1: Can a file contain more than one NEXUS record (i.e. concatenation,
with more than one #NEXUS line)?
Q2: Can a NEXUS record/file contain more than one alignment (matrix block)?

If the answer to either of those is a "yes", then any example files
you could contribute would be very helpful.

I have a more complicated question too, which would help me to resolve Bug 2227:
http://bugzilla.open-bio.org/show_bug.cgi?id=2227

Q3: Given a generic Alignment object (e.g. from one of the other
parsers), can I construct a corresponding Nexus object where the
aligned sequences are used for the matrix?  If so, how?

Thank you,

Peter