[Phylobase-devl] NCL and Mr. Bayes output

[Johan Nylander]

Hi,

On Sat, 2008-04-12 at 20:54 -0700, Peter Cowan wrote:

> [&W 0.000133] is not a valid command comment in a TREE command
> Line:   32
> Column: 54
> 
> Here is an example that causes this issue.  Does anyone know if this  
> *is* improper Nexus?  We might need a work around as it seems likely  
> that folks will want to read these files in (I do!).
> 

Can't answer to 100% since the NEXUS format seems to change constantly
(original NEXUS description from 1997, Maddison et al. Syst. Biol. does
only mention &R for rooted and &U for unrooted trees), but the &W
command is used in, e.g., current public version of PAUP to represent
tree weight. The use of it might be slightly different, however, from
the example given in the previous post. Note the use of fractions
instead of decimal numbers for the weights, and the occurrence of a
separate square-bracketed comment for the &W:

(from the output of 'boot treefile=file')

[Trees found in bootstrap replicate #10 (seed=1960800279)]
tree B_10.1 = [&U] [&W 1/2] (1,(((2,4),(3,8)),(5,(6,7))));
tree B_10.2 = [&U] [&W 1/2] (1,(((2,4),(5,(6,7))),(3,8)));


To summarize:
I believe you/we want to handle the weight command properly!

Yours
Johan Nylander