[Mesquitelist] Mesquite NEXUS file recognition

[Peter Midford]

Hi Eric,
             I agree with your general advice - I had suggested to Patrick (off-list) try to importing the file as a PHYLIP tree.  It seems to have worked.  I suggested that because the message indicated the first character was an '(', which in a phylogenetic context is mostly likely a Newick tree (and using the PHYLIP import is the general recommendation for loading bare Newick trees into Mesquite).  Nexus files are supposed to start with '#Nexus' and Mesquite will reject files that don't start with this token.

Apart from tricks like this, I agree that using a text editor is sometimes the only way to resolve broken nexus files (but it is easy to make bigger messes as well).

Cheers,

Peter

On Jan 5, 2012, at 2:13 PM, Eric Chapman wrote:

> Hi Patrick,
> 
> I have one general troubleshooting procedure that has gotten me around
> many problems of the type you are describing. Open the troublesome
> file with a text editor side-by-side with another nexus file
> (containing a tree) that gives Mesquite no problems and compare the
> formatting statements. If you do this, it may become perfectly obvious
> what the problem is. If you are new to this game, you may not be aware
> that these types of files (e.g., nexus, fasta, phylip, etc...) are all
> plain text files and a good text editor is a phylogeneticist's best
> friend.
> 
> Someone more familiar with this exact error message may be able to
> offer more specific advice, but doing the above may be all you need...
> 
> Eric Chapman
> 
> -- 
> Eric G. Chapman
> Post-doctoral Scholar
> Department of Entomology
> University of Kentucky
> S225 Agricultural Science Center N
> Lexington KY 40546-0091 USA
> (859) 257-2759 (lab)
> (330) 221-7812 (mobile)
> 
> 
> On Wed, Jan 4, 2012 at 10:40 PM, Patrick Moldowan <pmoldowa at uoguelph.ca> wrote:
>> To members of the Mesquite list,
>> 
>> As a component of my undergraduate thesis I have been composing a phylogeny of anuran amphibians.  A recent publication from Pyron and Wiens (2011) has been of great assistance in resolving amphibian classification, especially of the species I am interested in.  Dr. Pyron passed along the NEXUS file of this work, although I have encountered many difficulties when opening the file and accessing the tree for modification.
>> 
>> Specifically, while loading the file a window with the following message appears:
>> " Not a valid NEXUS file (first token is "(" "
>> 
>> Is there a specific statement of code that should precede all other coding text?  That is, what should precede the troublesome beginning parenthesis?
>> 
>> Pardon my ignorance, I am new to Mesquite and any advice on how to resolve the above message would be greatly appreciated.  Please let me know if I have been unclear or if further information is required to find a resolution.  I will be able to provide the NEXUS file if it would assist in troubleshooting.
>> 
>> All the best and continued success.  Thank you kindly in advance for your time, sincerely,
>> 
>> - Patrick Moldowan
>> --------------------------------------
>> Undergraduate, Hons. Wildlife Biology
>> University of Guelph
>> Guelph, ON
>> Canada
>> ------------------------------------------------------------------------------------------------------------------------------------
>> "There is grandeur in this view of life . . . from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved" - C. Darwin, The Origin of Species (1859)
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