Hello,

I did an analysis with MrBayes version 3.2.6 (Ronquist et al., 2012) with the GTR + G + I model with these commands

;

END;Begin mrbayes;

outgroup polyzona;

lset   nst = 6   rates = invgamma; prset statefreqpr=fixed(equal);

mcmc samplefreq=100 printfreq=100

nchains=4   Starttree=random  savebrlens=yes  filename=Antrodia-sl(complet).nex   ngen=8000000;

sumt filename=Antrodia-sl(complet).nex  nruns=2   ntrees=1  burnin=20000;

I want to know if I have all the commands for the GTR + G + I model and also if I get the majority rule consensus tree as a result?

To finish, I took MrBayes version 3.2.6 (Ronquist et al., 2012) and I wondered if I have the same thing as: Bayesian inference was calculated with MrBayes 3.1.2 with a general time reversible (GTR) model of DNA substitution and a gamma distribution rate variation across sites (Ronquist and Huelsenbeck 2003). 

I relied on the article Han et al. 2016 attached.

Thank you in advance.

Serge Audet

LITERATURE CITED

A. Rambaut, FigTree v1.4.2, A Graphical Viewer of Phylogenetic Trees. Available from 〈http://tree.bio.ed.ac.uk/software/figtree/〉,2014.

Han, ML; Chen, YY; Shen, LL; Song, J; Vlasák, J; Dai, YC; Cui, BK. 2016. Taxonomy and phylogeny of the brown-rot fungi: Fomitopsis and its related genera. Fungal Diversity. 80:343-373.

Nicholas KB, Nicholas HB Jr (1997) GeneDoc: a tool for editing and annotating multiple sequence alignments. Distributed by the authors. http://www.psc.edu/ biomed/genedoc.

Ronquist, Fredrik & Teslenko, Maxim & Mark, Paul & Ayres, Daniel & Darling, Aaron & Höhna, Sebastian & Larget, Bret & Liu, Liang & Suchard, Marc & Huelsenbeck, John. (2012). MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic biology. 61. 539-42. 10.1093/sysbio/sys029.