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How To A Make Bayesian Tree

The document provides instructions for making a Bayesian tree using MrBayes and FigTree software. It involves downloading and installing MrBayes and FigTree, running an MCMC analysis in MrBayes to estimate the posterior probability distribution, summarizing parameter values and trees from MrBayes, and opening the output file in FigTree to view the resulting Bayesian tree.

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Vinay Kumar Singh
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128 views5 pages

How To A Make Bayesian Tree

The document provides instructions for making a Bayesian tree using MrBayes and FigTree software. It involves downloading and installing MrBayes and FigTree, running an MCMC analysis in MrBayes to estimate the posterior probability distribution, summarizing parameter values and trees from MrBayes, and opening the output file in FigTree to view the resulting Bayesian tree.

Uploaded by

Vinay Kumar Singh
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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How to a make Bayesian Tree

 Firstly download JAVA ( https://www.java.com/en/download/ ).


 Then MrBayes (
https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/MrBayes-3.2.7-WIN.zip
).
 Then FigTree
(https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree.v1.4.4.zip )

Let’s start:
Concatenated File  Convert it to in ‘nexus’ format  Save it to in the same directory as
MrBayes. Open MrBayes.

1. At the MrBayes > prompt, type execute <your file name e.g. primates.nex>. This will bring the data
into the program. When you only give the data file name (primates.nex), MrBayes assumes that the file is
in the current directory. If this is not the case, you have to use the full or relative path to your data file, for
example execute ../examples/primates.nex.
2. At the MrBayes > prompt, type lset nst=6 rates=invgamma. This sets the evolutionary model to the
GTR substitution model with gamma-distributed rate variation across sites and a proportion of invariable
sites.

3. At the MrBayes > prompt, type mcmc ngen=20000 samplefreq=100 printfreq=100 diagnfreq=1000.
This will start the Markov chain Monte Carlo simulation. It will also ensure that you get at least 200
samples from the posterior probability distribution, and that diagnostics are calculated every 1,000
generations. For larger data sets you probably want to run the analysis longer and sample less frequently.
The default sample and print frequency is 500, the default diagnostic frequency is 5,000, and the default
run length is 1,000,000. You can find the predicted remaining time to completion of the analysis in the
last column printed to screen.
4. 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.
5. 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.
Make sure that the potential scale
reduction factor (PSRF) is
reasonably close to 1.0 for all
parameters; if not, you need to run
the analysis longer. The same
applies for the effective sample size
(ESS). If the ESSs are somewhere
below 100, you may want to run
longer.

6. Summarize the trees using the


same burn-in as the mcmc
command by typing 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 (Rambaut and
Drummond, 2012) and other tree-
drawing programs, such as
TreeView (Page, 1996) and
Mesquite (Maddison and Maddison,
2006).
Open FigTree > Open file ‘’your file name.nexus.con’’.

Here is your Bayesian Tree.

Make sure ‘Node labels’ box is ticked

####

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