Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
specifying the matrix (Read 2419 times)
kateveronica
YaBB Newbies
*
Offline


I love YaBB 1G - SP1!

Posts: 2
specifying the matrix
Nov 7th, 2006 at 9:02am
 
Hey Guys,
I am a newby to hyphy and bioinformatics as a whole. I was following the tutorial. After partiitioning the data for p_51.nex sample data, I chose the p_51 tree and tried to specify the substitution/matrix model to be HKY85 inorder to be able to get a likelihood function. My only choice when I went to the dropdown menu was "none". the Likelihood function cannot be carried out without out a tree and a "model". What am I missing here? Thanks,
Kate
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: specifying the matrix
Reply #1 - Nov 7th, 2006 at 9:20am
 
Dear Kate,

My first guess would be that HyPhy is not reading model definitions from its install directory. You can check this by opening the Object Inspector, and looking under the Models tab to see if there are some models (including HKY85) listed there.

What OS are you running HyPhy under?

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
 
kateveronica
YaBB Newbies
*
Offline


I love YaBB 1G - SP1!

Posts: 2
Re: specifying the matrix
Reply #2 - Nov 7th, 2006 at 4:03pm
 
Sorry, I meant to include what OS I am using in the original question. Mine is Mac OS X 10.4.8. Does that mean something regarding hyphy? I will try your suggestion and bug you again if I still have problems. Thanks alot for your help,
kate
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: specifying the matrix
Reply #3 - Nov 7th, 2006 at 4:22pm
 
Dear Kate,

The OS determines (to an extent) how HyPhy decides where to look for its components.

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