Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
Likelihood function constraints (Read 1790 times)
Nick1979
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 6
Houston
Gender: male
Likelihood function constraints
Jun 17th, 2013 at 9:19am
 
Hi Sergei,

I am new at this and would greatly appreciate if you check my code. I have two aligned sequences and i want to test whether the three codon sites evolve at equal rates.

I have attached my code


  Thank you












Back to top
« Last Edit: Jun 17th, 2013 at 12:45pm by Nick1979 »  
Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login (2 KB | 8 )
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: Likelihood function constraints
Reply #1 - Jun 24th, 2013 at 8:45pm
 
Hi Nick,

Your code looks good, apart from the fact that comments in HyPhy are C-style ( '//' or '/* */' ), and not Perl (#) style.
One minor point is that in your code, the branch lengths are still slightly different even AFTER you constrain 'b', because the base frequencies are different among partitions.

You could uses pooled base frequencies among all partitions (i.e. the same HKY85 model) which doesn't have this issue; if you need to maintain different sets of frequencies, some transformations of 'b' are required (see the attached file).

Sergei

Back to top
 
Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login (3 KB | 4 )

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