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 <[email protected]> > 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 > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
