# Computer software

## Tutorials for Windows and MAC OSX/Linux/Unix command line

The best way of running the programs here is by the command line.
Since some modern students have never seen the command line, I have
written some notes to introduce the basics. I suggest that you go
through the tutorial yourself before trying to run the programs like
paml or bpp. I think the tutorial should take less than one hour.
Please let me know if you find the tutorial confusing or if you have
comments or suggestions.

Tutorial for Microsoft Windows command line, pdf, 4 pages

Tutorial for MAC OSX/Linux/Unix command line, pdf, 4 pages

An fairly extensive Introduction
to Unix commands, written by Tim Massingham for the Workshop on Computational
Molecular Evolution (CoME), pdf, 28 pages.
Yang, Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.

Yang, Z. 2007 PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24, 1586-1591.
## BP&P: Bayesian analysis of genomic sequence data under the
multispecies coalescent model

The program BP&P
(bpp3.2.tgz) implements a series of Bayesian inference methods
under the multispecies coalescent model. The analyses may include
estimation of population size (theta's) and species divergence times
(tau's), species tree estimation and species delimitation. Windows
executables and C source code (for unix/linux/macosx) are all in the
same archive. Here is a pre-compiled version for mac osx 7 and later
(bpp3.1.macosx.tgz).
Please read the documentation before you use this program. The
following paper includes a tutorial that works for both bpp 3.1 and 3.2.
Yang, Z. 2015. A tutorial of BPP for species tree estimation and
species delimitation. Current Zoology 61:854-865. pdf

BP&P replaces the old program MCMCcoal,
which implements the Bayesian method of Rannala & Yang (2003) and
Burgess & Yang (2008).
Bo Xu has written a graphics user interface for BPP, called bppX. The
compiled executables are here for Windows, Mac OSX, and linux. You install (unpack and
compile) the current version of bpp first. Then unpack the GUI bppX.
Then go to Function-Configuration to specify the folder name for the
bpp files.
Questions and discussions about bp&p should go to this link.

The program 3s implements likelihood ratio tests to test for gene flow between two closely related species. Click on the link above for more information.

The archive name is mb3.2.1.Dir.tgz. This is a modified version of
MrBayes Version 3.2.1, modified to use the Gamma-Dirichlet and Inverse
Gamma-Dirichlet priors for branch lengths (Rannala et al. in press;
Zhang et al. 2012). This also includes the two exponential priors on
internal and external branch lengths described by Yang & Rannala
(2005) and Yang (2007). There is a brief description of the changes
in the file mb3.2.Dirichlet.Notes.pdf inside the archive.
If you use the modified program, please cite MrBayes as well as the
papers that describe the modifications.
Yang, Z 2007 Fair-balance paradox, star-tree paradox and Bayesian phylogenetics. Mol. Biol. Evol. 24, 1639-1655.

Yang, Z & Rannala, B. 2005 Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol. 54, 455-470.

Rannala, B., T. Zhu, and Z. Yang. 2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.

Zhang, C., B. Rannala, and Z. Yang. 2012. Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Syst. Biol. 61:779-784.

## oncoSpectrum v1.2: ML program for estimating mutation rates using cancer mutation databases.

Yang Z, Ro S, Rannala B. 2003. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 165:695-705.

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