Difference between revisions of "Phycas Home"

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'''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.
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'''Phycas''' is a Python extension for carrying out Bayesian phylogenetic analyses.  
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<!-- The current version (2.0.0) was posted here July 12, 2014. -->
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<!-- The current version (2.0.1) was posted here August 5, 2014. -->
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<!-- The current version (2.1.0) was posted here August 13, 2014. -->
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The current version (2.2.0) was posted here December 14, 2014.
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While it should be possible to build Phycas on most Linux systems, we can only provide pre-built versions for a couple of different combinations of operating system and Python version.
  
=== New version coming soon... ===
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== Manual ==
  
A new version of Phycas will be posted soon that implements the Stepping Stone and CPO methods discussed at the Evolution 2010 meetings in Portland, Oregon, June 27, 2010. These methods are not present in version 1.1.2, however.
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* Download [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/phycas-manual-2.2.0.pdf phycas-manual-2.2.0.pdf]
  
=== New version 1.1.2 posted March 13, 2009 ===
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== Pre-built version for MacOS 10.9 (Mavericks) ==
  
This is a bug-fix release. Please replace version 1.1 or version 1.1.1 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 [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/BUGS BUGS] file for details).
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# Download [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/phycas-2.2.0-mac.tar.gz phycas-2.2.0-mac.tar.gz]
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# Follow directions in the manual to install
  
Phycas version 1.1.2 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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== Pre-built 32-bit version for Windows 7/8, Python 2.7 ==
  
[[Phycas Development Team]]
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# Download [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/phycas-2.2.0-win.zip phycas-2.2.0-win.zip]
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# Follow directions in the manual to install
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== Build from source on Linux ==
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# Download [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/phycas-2.2.0-src.tar.gz phycas-2.2.0-src.tar.gz]
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# Download [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/INSTALL INSTALL]
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# Follow directions in the INSTALL file to build a version from source
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== Problems? ==
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Version 2.0 was a major revision, and we have changed the way we distribute Phycas, so it is quite possible that there are glitches that need to be worked out. If you have problems getting Phycas to work, please write to [mailto:paul.lewis@uconn.edu Paul Lewis].
  
 
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=== New version 1.2.0 posted August 9, 2010 ===
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Phycas version 1.2.0 can be downloaded for Windows or Mac on the [[Download]] page. (Linux versions are also available but must be compiled from the C++ sources.) New features include support for data partitioning and the generalized stepping stone method for estimating marginal likelihoods.
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[[Phycas Development Team]]
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=== Current version 1.1.2 posted March 13, 2009 ===
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This is a bug-fix release. Please replace version 1.1 or version 1.1.1 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 [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/BUGS BUGS] file for details).
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Phycas version 1.1.2 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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=== New version 1.1.1 posted March 12, 2009 ===
 
=== New version 1.1.1 posted March 12, 2009 ===
  

Latest revision as of 02:30, 27 August 2015

Phycas is a Python extension for carrying out Bayesian phylogenetic analyses. The current version (2.2.0) was posted here December 14, 2014. While it should be possible to build Phycas on most Linux systems, we can only provide pre-built versions for a couple of different combinations of operating system and Python version.

Manual

Pre-built version for MacOS 10.9 (Mavericks)

  1. Download phycas-2.2.0-mac.tar.gz
  2. Follow directions in the manual to install

Pre-built 32-bit version for Windows 7/8, Python 2.7

  1. Download phycas-2.2.0-win.zip
  2. Follow directions in the manual to install

Build from source on Linux

  1. Download phycas-2.2.0-src.tar.gz
  2. Download INSTALL
  3. Follow directions in the INSTALL file to build a version from source

Problems?

Version 2.0 was a major revision, and we have changed the way we distribute Phycas, so it is quite possible that there are glitches that need to be worked out. If you have problems getting Phycas to work, please write to Paul Lewis.