MrBayes Tree

Use clustalw to generate nexus format file

#NEXUS
BEGIN DATA;
dimensions ntax=55 nchar=534;
format missing=?
symbols=”ABCDEFGHIKLMNPQRSTUVWXYZ”
interleave datatype=DNA gap= -;

Change to as follows:
#NEXUS
BEGIN DATA;
dimensions ntax=55 nchar=534;
format datatype=dna interleave=yes gap=- missing=?;

then type mb -i *.nex

MrBayes > lset nst=6 rates=invgamma

Setting Nst to 6
Setting Rates to Invgamma
Successfully set likelihood model parameters

MrBayes > mcmc ngen=20000 samplefreq=100 printfreq=100 diagnfreq=1000

Setting number of generations to 20000
Setting sample frequency to 100
Setting print frequency to 100
Setting diagnosing frequency to 1000
Running Markov chain
MCMC stamp = 4956565474
Seed = 1367482907
Swapseed = 1367482907
Model settings:

………
MrBayes > sump
Type sump to summarize the parameter values using the same burn-in as
the diagnostics in the mcmc command. The program will output a table with
summaries of the samples of the substitution model parameters, including the
mean, mode, and 95 % credibility interval (region of Highest Posterior Density,
HPD) of each parameter.

MrBayes > sumt
The program will output a cladogram with the posterior
probabilities for each split and a phylogram with mean branch lengths. Both
trees will also be printed to a file that can be read by FigTree and other
tree-drawing programs, such as TreeView and Mesquite.

Note:
If the standard deviation of split frequencies is below 0.01 after 20,000
generations, stop the run by answering no when the program asks Continue the
analysis? (yes/no). Otherwise, keep adding generations until the value falls
below 0.01. If you are interested mainly in the well-supported parts of the tree, a
standard deviation below 0.05 may be adequate.

converting file formats
Having the proper data file format is essential as many programs can only input certain file types. The following are some of the input and output file formats for specific programs.

CLUSTAL file format:
Programs that input this file type: Clustal W/X
Programs that output this file type: Clustal W/X

FASTA file format:
Programs that input this file type: Clustal W/X, MAFFT
Programs that output this file type: Clustal W/X, MAFFT

NEXUS file format:
Programs that input this file type: BEAUti, GARLI, Modeltest, MrBayes, PAUP*
Programs that output this file type: Clustal W/X, PAUP*

PHYLIP file format:
Programs that input this file type: GARLI, LAMARC, Migrate-n, PAML, PHYLIP
Programs that output this file type: Clustal W/X, PAUP*, PHYLIP

PIR file format:
Programs that input this file type: Clustal W/X
Programs that output this file type: Clustal W/X