[Bioperl-l] root node branch length in newick trees written incorrectly

Dave Messina David.Messina at sbc.su.se
Thu Apr 1 08:41:23 EDT 2010


Hi everyone,

It seems that TreeIO::newick might not be properly writing root nodes which have a branch length — it omits the colon.

e.g.

If you read in

	(a:1,b:2):0.0;

It will be written out as

	(a:1,b:2)0.0;


And in the latter case, 0.0 now looks like a node id, causing strict interpreters of newick (like PAML) to complain.

Crazy for the root to have a branch length, you say? Apparently it's a matter of taste — RAxML and TreeAlign do it, and according to the newick spec it's legit.*

I just filed a bug report (http://bugzilla.open-bio.org/show_bug.cgi?id=3039) with a patch and a test.

But I'm not sure I understand the code that well,though; could another dev or two take a look before I commit?


Thanks,
Dave




* See the example at the bottom of http://evolution.genetics.washington.edu/phylip/newick_doc.html




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