1 min read

jmodeltest will not run with single quotes around tip names

A little while ago, I discovered a common error in jmodeltest is the error message that the number of sites appears to be wrong.  I recently encountered this issue again.  This is caused by single quotation marks on either side of tip names in a NEXUS file, which is a common form of the output / exported NEXUS file from DNASP. 

So, once you export a NEXUS from DNASP, say after doing some population level genetic analyses or after defining sequence groups for setting up structure in ARLEQUIN, you should simply open your NEXUS file in a word processor or text editor and use the “Replace” command to remove all quotation marks from your file.  Dots aren’t usually a problem, but spaces should probably also be avoided within sequence names.  I never put spaces, only letters, numbers, dots, or underscores.  And this has worked for me so far.  Hope this helps.

~ J