Question: Mr. Bayes Protein Models
1
gravatar for kanwalashraf07
8 months ago by
kanwalashraf0710 wrote:

Hello, I am using Mr. Bayes for my amino acid data set, The model predicted by prottest is rtRev + G + I. I can specify rtRev on mr bayes by using "prset aamodelpr=fixed <...>" , However, I am not sure how can I implement G + I. Any help will be much appreciated... :)))

ADD COMMENTlink modified 8 months ago by arnstrm400 • written 8 months ago by kanwalashraf0710
0
gravatar for Whetting
8 months ago by
Whetting1.1k
Bethesda, MD
Whetting1.1k wrote:

would you not just "lset rates=invgamma"?
www.molecularevolution.org/molevolfiles/mrbayes/Appendix_Fig2.pdf‎ )

ADD COMMENTlink written 8 months ago by Whetting1.1k
0
gravatar for arnstrm
8 months ago by
arnstrm400
Ames, IA
arnstrm400 wrote:

Here is the list for your reference:

I    : lset rates=propinv;
G    : lset rates=gamma;
F    : prset statefreqpr=fixed(empirical);
I + G    : lset rates=invgamma;
G + F    : prset statefreqpr=fixed(empirical); lset rates=gamma; 
I + F    : prset statefreqpr=fixed(empirical); lset rates=propinv;
I + G + F    : prset statefreqpr=fixed(empirical); lset rates=invgamma;

I also add these to my mb code block

mcmcp ngen=1000000 nchains=4 printfreq=100 samplefreq=100 burnin=200; # Number of cycles, sampling/printing frequency and burnin
mcmc; # mcmc analysis
sump; # summarized parameters
sumt; # summarized trees
quit

EDIT: fixed I + G typo

ADD COMMENTlink modified 8 months ago • written 8 months ago by arnstrm400

Are you sure? I believe I+G is invgamma...?! (http://bodegaphylo.wikispot.org/MrBayes_Tutorial)

ADD REPLYlink written 8 months ago by Whetting1.1k

sorry, my bad! it was a bad copy/paste job. Fixed it now, thanks.

ADD REPLYlink modified 8 months ago • written 8 months ago by arnstrm400
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