[Phylobase-devl] NCL and Mr. Bayes output

Peter Cowan pdc at berkeley.edu
Mon Apr 14 01:48:05 CEST 2008


Ben,

Yes, it now works.  I would vote for being in contact with Paul Lewis,  
if the code bases drift from each other it will make things more  
difficult in the future.

Also, NexusToPhylo4() is about half the speed of read.nexus() on a  
file with 250 trees, and worse with larger files.

I've made one small enhancement (~10%) that I am testing.

I can't really tell what's going on, but it looks like NCL returns a  
list, that is then parsed with regular expressions.  What exactly does  
the NCL code do to the file?

Peter

On Apr 13, 2008, at 7:51 AM, Ben Bolker wrote:
> 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
>> _______________________________________________
>> Phylobase-devl mailing list
>> Phylobase-devl at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
>
>



More information about the Phylobase-devl mailing list