HyPhy message board - How to mention the name of the nucleotide evolutionary model

	Welcome, Guest. Please Login

Home

Help

HyPhy message board › HYPHY Package › HyPhy feedback › How to mention the name of the nucleotide evolutionary model

(Moderators: Sergei, Simon)

‹ Previous Topic | Next Topic ›

Pages: 1

Send Topic

How to mention the name of the nucleotide evolutionary model (Read 6936 times)

RTuteja

YaBB Newbies

Offline

Curious HyPhy user

Posts: 13
Ireland
Gender: female

How to mention the name of the nucleotide evolutionary model
Nov 5^th, 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

IP Logged

Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: How to mention the name of the nucleotide evolutionary model Reply #1 - Nov 5^th, 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; (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 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 12^th, 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

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 13^th, 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

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

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 16^th, 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-------

IP Logged

RTuteja YaBB Newbies Offline Curious HyPhy user Posts: 13 Ireland Gender:	Re: How to mention the name of the nucleotide evolutionary model Reply #5 - Nov 19^th, 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:	Re: How to mention the name of the nucleotide evolutionary model Reply #6 - Nov 19^th, 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 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 4^th, 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

Pages: 1

Send Topic

‹ Previous Topic | Next Topic ›

« Home

‹ Board

Top of this page