[Mesquitelist] Mesquite NEXUS file recognition

[Eric Chapman]

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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