P4 is a Python package for maximum likelihood and Bayesian analysis of molecular sequences.
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Anaphory/p4-phylogeny
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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.
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P4 is a Python package for maximum likelihood and Bayesian analysis of molecular sequences.
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