MrBayes

The Building Phylogenetic Tree dialog for the MrBayes method has the following view:

There are two steps to a phylogenetic analysis using MrBayes:

Set the evolutionary model.
Run the Markov chain Monte Carlo (MCMC) analysis.

The evolutionary model is defined by the following parameters:

Substitution model — specifies the general structure of a DNA substitution model. This parameter is available for nucleotide sequences. It corresponds to the Nst setting of MrBayes. You may select one of the following:

JC69 (Nst=1)
HKY85 (Nst=2)
GTR (Nst=6)

Rate matrix (fixed) — specifies the fixed-rate amino-acid model. This parameter is available for amino-acid sequences. The following models are available:

poisson
jones
dayhoff
mtrev
mtmam
wag
rtrev
cprev
vt
blosum
equaline

The following parameters are common for nucleotide and amino-acid sequences:

Rate — sets the model for among-site rate variation. Select one of the following:

equal — no rate variation across sites.
gamma — gamma-distributed rates across sites. The rate at a site is drawn from a gamma distribution. The gamma distribution has a single parameter that describes how much rates vary.
propinv — a proportion of the sites are invariable.
invgamma — a proportion of the sites are invariable while the rate for the remaining sites is drawn from a gamma distribution.

Gamma — sets the number of rate categories for the gamma distribution.

You can select the following parameters for the MCMC analysis:

Chain length — sets the number of cycles for the MCMC algorithm. This should be a large number as you want the chain to first reach stationarity and then remain there for enough time to take many samples.

Subsampling frequency — specifies how often the Markov chain is sampled. You can sample the chain every cycle, but this results in very large output files.

Burn-in length — determines the number of samples that will be discarded when convergence diagnostics are calculated.

Heated chains — specifies the number of chains used in Metropolis coupling. Set to 1 to use the usual MCMC analysis.

Heated chain temp — the temperature parameter for heating the chains. The higher the temperature, the more likely the heated chains are to move between isolated peaks in the posterior distribution.

Random seed — a seed for the random number generator.

Display tree in new window — displays the tree in a new window.

Display tree with alignment editor — displays the tree with the alignment editor.

Synchronize alignment with tree — synchronizes the alignment and tree.

Save tree to — specifies the file to save the built tree.

Press the Build button to run the analysis with the selected parameters and build a consensus tree.