Difference between revisions of "Phycas Home"

From Phycas
Jump to: navigation, search
 
(32 intermediate revisions by the same user not shown)
Line 1: Line 1:
'''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.
+
'''Phycas''' is a Python extension for carrying out Bayesian phylogenetic analyses.  
 +
<!-- The current version (2.0.0) was posted here July 12, 2014. -->
 +
<!-- The current version (2.0.1) was posted here August 5, 2014. -->
 +
<!-- The current version (2.1.0) was posted here August 13, 2014. -->
 +
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.
  
Phycas is still in active development and should be considered '''alpha software'''. We will be demonstrating the program August 5, 2008, at the [http://workshop.molecularevolution.org/mbl/ Woods Hole Workshop on Molecular Evolution], and we plan to release the version used in this workshop by the end of the first week of August.
+
== Manual ==
 +
 
 +
* Download [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/phycas-manual-2.2.0.pdf phycas-manual-2.2.0.pdf]
 +
 
 +
== Pre-built version for MacOS 10.9 (Mavericks) ==
 +
 
 +
# 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]
 +
# Follow directions in the manual to install
 +
 
 +
== Pre-built 32-bit version for Windows 7/8, Python 2.7 ==
 +
 
 +
# Download [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/phycas-2.2.0-win.zip phycas-2.2.0-win.zip]
 +
# Follow directions in the manual to install
 +
 
 +
== Build from source on Linux ==
 +
 
 +
# 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]
 +
# Download [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/INSTALL INSTALL]
 +
# 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 [mailto:paul.lewis@uconn.edu Paul Lewis].
 +
 
 +
<!--
 +
=== New version 1.2.0 posted August 9, 2010 ===
 +
 
 +
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.
  
 
[[Phycas Development Team]]
 
[[Phycas Development Team]]
 +
 +
=== Current version 1.1.2 posted March 13, 2009 ===
 +
 +
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).
 +
 +
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.)
 +
 +
=== 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 [http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/BUGS 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.)
 +
 +
=== Version 1.1 posted February 11, 2009 ===
 +
 +
<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>
 +
 +
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.
 +
-->

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.