[Phylobase-devl] NCL and Mr. Bayes output

[Ben Bolker]

   It was fairly easy to hack nxstreesblock.cpp to silently
ignore &W / weights statements (just committed this to SVN);
we should give further thought to how to make it work right.
Should we add a "weights" element to the multi-tree object??

   Brian, do you have any sense of how hard it would
be too get the ncl code to pay attention to this?
Is it worth relaying this back to the ncl author?

   Ben


Johan Nylander wrote:
> 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
> 
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