i have just downloaded the windows version your program. When I try to run the Yang-Neilsen method to tst for positive selection, my input data nexus file is recognised by my treefile continually causes the following error and the program to crash. I exported my treefile from Paup*

'Node names should begin with a letter, a number, or an underscore. Had: #?Nexus. current BL Command:treeString=RerootTree(treeString,0) Current task has been terminated'

Can you explain this and tell me how to fix it.

Thanks!!

Dear Allison,

The crash shouldn't happen:) I'll see if I can reproduce the error. Generally speaking, HyPhy expects a tree file which contains only the Newick tree string (e.g. no NEXUS or other wrappers). Try editing the tree file output by PAUP* to only include the tree string. Alternatively, if your input datafile (NEXUS, FASTA etc), already contains a tree (together with the sequence data), HyPhy will read it and offer the option to use that in the analysis.

Lastly, we also recommend that analyses for positive selection be done with models which allow both synonymous and non-synonymous rates to vary along the sequence. The reference papers for this are Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login and Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login. HyPhy how to is in the second post (for REL) in this thread Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Cheers,
Sergei