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p4
==

P4 does Bayesian and maximum likelihood phylogenetic analyses on
molecular sequences.  It's specialty is that you can use heterogeneous
models, where the model parameters can differ in different parts of
the tree, or over different parts of the data.

The user interface for p4 is the Python language.  That means that p4
comes with all the abilities of a high-level object-oriented
programming language.  This is a Good Thing.

I have successfully installed it on linux and on Mac OS X.

Thanks to Dave Swofford and Ziheng Yang for some code.

Many of the ideas were influenced or stolen from the excellent
MrBayes, and thanks are given to the authors, John Huelsenbeck and
Fredrik Ronquist.

Getting Started
---------------

To install it, see the file INSTALL.rst

Once you have it installed, call it from your command line, eg

yourShellPrompt% p4

and read the splash screen.  It will invite you to read the
func.info() and it will tell you where some examples are installed.
Try the examples, and make variations on them.  Python help() within
p4, eg

p4> help(Mcmc)

will give a lot of documentation.

Citation
--------
Foster, P.G. 2004.  Modeling compositional heterogeneity.  Syst. Biol. 53: 485-495.


Using build.xml
---------------

This needs pyAntTasks-X.X.jar installed in /usr/share/ant/lib, if it is not already.  I had to use a slightly older version (1.2) on my mac using native java, as the mac java was so old.