Phylogenetic Utility Programs
Phylogenetic Utility Programs
Programs to aid in the summary of the posterior distribution of phylogenetic trees from the program
MrBayes are provided. They are
- post_prob: This program will tabulate the percentage of times each tree topology appears in the
posterior distribution output by MrBayes, thus providing posterior probabilities for each tree topology.
Reference: Huelsenbeck, J. and F. Ronquist. 2001.
MRBAYES: Bayesian inference of phylogenetic trees.Bioinformatics17(8):754-755.
Download: post_prob.c, post_prob.h
- post_root: This program will tabulate the percentage of times each possible root position appears in the posterior
distribution output by MrBayes, thus providing posterior probabities
for each root. Updated 22 Oct 2007
Reference: Huelsenbeck, J., J. Bollback, and A. Levine. 2002. Inferring the root of a phylogenetic trees.
Systematic Biology 51(1): 32-43.
Download:
Each of these programs takes as its input
the tree file output by MrBayes (which ends in *.out.t, where *=the name of the input file),
though this file must
be copied to the file posttrees and the nexus block converting taxon names to numbers must be removed.
A new line
must be added which contains the number of sequences and the number of trees in the file. post_prob creates a file
called treefile that contains Newick formatted trees with their frequency in the posterior distribution, as well
as displaying summary information to standard output. All of the results of post_root are displayed to
standard output.
The source code for each program (in C) can be downloaded by clicking on the links above. They will
need to be compiled on your particular system.
Here is a sample posttrees file.
- root_diag: This program will create the data necessary to construct the
root diagnostic described in Boykin et al. (2006). The program post_root must be placed
in the same directory as this program and compiled prior to running root_diag. The
program will prompt the user at the command line for relevant
information. Updated 22 Oct 2007
Reference: Boykin, L., L. Salter, and T. Lowrey. 2006. Phylogenetic relationships of Orcuttieae (Poeaceae: Chloridoideae): Utility of Bayesian rooting methods, in revision.
Download: root_diag.c
This program takes as its input
the tree file output by MrBayes (which ends in *.out.t, where *=the name of the input file),
though this file must
be copied to the file posttrees and the nexus block converting taxon names to numbers must be removed. The iterations discarded
as burnin must also be removed (if they were originally saved by MrBayes). root_diag creates two files: rootpp.dat, which gives posterior probabilities
for all root positions for all iterations; and rootdiag.dat contains the information
required to create a convergence plot for the root position of interest.
- Sample R function to compute convergence diagnostics from *.nex.p files produced by MrBayes. Used in the
following paper:
Boykin, L., L. Salter, and T. Lowrey. 2006. Phylogenetic relationships of Orcuttieae (Poeaceae: Chloridoideae): Utility of Bayesian rooting methods.
Download: diag.r
Please note: This is meant to be an example only, for those who have some familiarity with R. It would
need to be modified considerably for any specific application.
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