Difference between revisions of "Phycas Home"
From Phycas
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Phycas version 1.1.1 can be downloaded for Windows or Mac on the [[Download]] page. (Linux versions are available but must be compiled from the C++ sources.) | Phycas version 1.1.1 can be downloaded for Windows or Mac on the [[Download]] page. (Linux versions are available but must be compiled from the C++ sources.) | ||
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| + | === Version 1.1 posted February 11, 2009 === | ||
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<div style="color: red">A bug affects the current version (1.1) of Phycas, causing log-likelihoods to be inaccurate under some circumstances. We are currently working on identifying the cause of the problem, and will post a new version when the problem has been fixed.</div> | <div style="color: red">A bug affects the current version (1.1) of Phycas, causing log-likelihoods to be inaccurate under some circumstances. We are currently working on identifying the cause of the problem, and will post a new version when the problem has been fixed.</div> | ||
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Two new commands (ps and sump) are included in this release. The ps command implements path sampling (a.k.a. thermodynamic integration) and a new method steppingstone sampling, both of which are used to estimating marginal likelihoods for models (the Bayes factor used to compare models is a ratio of marginal likelihoods). The sump command is analogous to the command of the same name in MrBayes. | Two new commands (ps and sump) are included in this release. The ps command implements path sampling (a.k.a. thermodynamic integration) and a new method steppingstone sampling, both of which are used to estimating marginal likelihoods for models (the Bayes factor used to compare models is a ratio of marginal likelihoods). The sump command is analogous to the command of the same name in MrBayes. | ||
Phycas version 1.1 is no longer available for download because newer versions are available. | Phycas version 1.1 is no longer available for download because newer versions are available. | ||
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[[Phycas Development Team]] | [[Phycas Development Team]] | ||
Revision as of 20:34, 12 March 2009
Phycas is a Python application for carrying out phylogenetic analyses. Phycas is also a C++ and Python library that can be used to create new applications or to extend the current functionality.
New version 1.1.1 posted March 12, 2009
This is a bug-fix release. Please replace version 1.1 with this version to avoid the use of possibly incorrect likelihoods under invariant sites models or (for any model) trees with more than 26 taxa (see description of the "underflow" bug in BUGS file for details).
Phycas version 1.1.1 can be downloaded for Windows or Mac on the Download page. (Linux versions are available but must be compiled from the C++ sources.)
