[Biojava-l] ParseException when using interleaved Nexus file

[David Johnson]

Hi Richard,

OK that's good to know... I suppose that's the problem with specifications -
people don't always follow them!

But I get the impression either some people think that using
interleave=yes/no is standard practice, or it could be being generated by
some other phylo software (e.g. maybe PAUP or some other tools).

I had a talk with my supervisor and he actually can't find the specific
programs that have been putting that in, but looking at a range of his Nexus
files, there's quite a few that seem to use put in the yes/no bits, some
files he received from other researchers.

Are the modifications available in the latest automated build (on
CruiseControl)?

Cheers,
-David

2009/8/11 Richard Holland <holland at eaglegenomics.com>

> I've found the problem - "interleave=yes" is not valid according to the
> official NEXUS format spec which the parser was written against. (Maddison
> et al., 1997)
>
> Interleaved file are supposed to only include the word "interleave" - it
> takes no parameters. Non-interleaved files shouldn't mention it at all.
>
> I've modified the parser to tolerate this but I'd be interested to know
> where the invalid token came from - was it added manually, or by an existing
> piece of publically available software?
>
> The modification has been made in the trunk of the biojava-live subversion
> repository.
>
> cheers,
> Richard
>
>
>