Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
How to mention the name of the nucleotide evolutionary model (Read 4869 times)
RTuteja
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 13
Ireland
Gender: female
How to mention the name of the nucleotide evolutionary model
Nov 5th, 2012 at 6:30am
 
Hi All,

Modelgenerator program has predicted that the best model for my sequences is TVM+I+G. I don't see this model in the menu while using singlebreakpointReco.

Can you please suggest me the way to specify this model. I don't know what is the six letter designation for the models.

Please help!

Thanks,
Reetu
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: How to mention the name of the nucleotide evolutionary model
Reply #1 - Nov 5th, 2012 at 1:36pm
 
Hi there,

TVM == REV with fixed (0.25) base frequencies.
Use (012345); see Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login; (page 16)

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
 
RTuteja
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 13
Ireland
Gender: female
Re: How to mention the name of the nucleotide evolutionary model
Reply #2 - Nov 12th, 2012 at 3:07am
 
Hi Seregi,

Thanks for your help so far on this.

I could not find why I have to specify TVM == REV, instead of only TVM (are these submodels?). I have around 200 gene families for analysis. I am reading up in the area of nucl evolutionary models but any suggestions/hints from you will be a helpful to explore myself further.

Many thanks for your help!

Regards,
Reetu
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: How to mention the name of the nucleotide evolutionary model
Reply #3 - Nov 13th, 2012 at 2:11pm
 
Hi Reetu,

Generally speaking, in most HyPhy analyses it is not terribly important to specify the exact "best" nucleotide model; so long as you don't force a model that's too simplistic (e.g. F81). REV is more general than TVM, and base frequencies in REV are not estimated as a part of the likelihood function (they are estimated by nucleotide counts), so it won't hurt much effect on the inference.

For some good background reading on the subject of model selection Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

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
 
RTuteja
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 13
Ireland
Gender: female
Re: How to mention the name of the nucleotide evolutionary model
Reply #4 - Nov 16th, 2012 at 10:01am
 
Hi Sergei,

I am getting the following error while running Singlebreakpint.bf module on cluster. Can you please help where I am doing mistake.

Thanks,
Reetu
+++++++++++++++++++++++++++++
2). Looking for a breakpoint...
Error:

Master node received an error:Cannot reuse the filter 'filteredData0' because it is already being used by likelihood function 'lf', and the two likelihood functions impose different leaf-to-sequence mapping. Create a copy the filter and pass it to the second likelihood function to resolve this issue.

Function call stack
1 : Construct the following likelihood function:filteredData0 ; givenTree1 ; filteredData1 ; givenTree0 ;
        Standard input redirect:
                Empty Associative List-------
2 : RunASample(individual)
        Standard input redirect:
                Empty Associative List-------
Back to top
 
 
IP Logged
 
RTuteja
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 13
Ireland
Gender: female
Re: How to mention the name of the nucleotide evolutionary model
Reply #5 - Nov 19th, 2012 at 4:51am
 
P.S.- If I skip the KH-test then everything is working fine. Is this a bug or I am making some mistake?
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: How to mention the name of the nucleotide evolutionary model
Reply #6 - Nov 19th, 2012 at 1:00pm
 
Hi Reetu,

I think this is a bug in the script. Let me investigate.

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
 
yuda
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 2
Re: How to mention the name of the nucleotide evolutionary model
Reply #7 - Oct 4th, 2013 at 2:33am
 
Dear Sergei,

I was wondering whether you could fix the bug in the SBP script.

Thank you,
Haruo
Back to top
 
 
IP Logged