[Biopython-dev] Bio.AlignIO, Bio.Nexus, MrBayes, polymorphic sites, maximum line length

[Peter]

On Thu, Dec 2, 2010 at 5:11 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:
> Peter wrote:
>>
>> Did you ask Bio.Nexus to write interleaved output?
>> I've got MrBayes 3.1.2, and this seems to fix your example:
>> ...
>> Does that work for you?
>>
>
> Hi Peter,
>
> Yes, that does the trick! I wonder if perhaps that's what Cymon meant
> to say rather than interleave_by_partition (hence the boolean problem) ?
>
> Excellent.

Could be - Cymon?

Are there any downsides to making Bio.AlignIO used interleaved
by default? I guess some tools may prefer non-interleaved output...
as a compromise we could switch depending on the number of
columns in the alignment?

Peter