Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
Uploading tree input file (Read 2207 times)
Allison
Guest


Uploading tree input file
Feb 22nd, 2006 at 7:48am
 
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!!
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: Uploading tree input file
Reply #1 - Feb 22nd, 2006 at 10:33am
 
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 Login and Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login 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 Login

Cheers,
Sergei
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged