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PHAST (Phylogenic Analysis with Space/Time Models)

Table of Contents

Introduction

PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel). For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

See the Software Versions page for the WestGrid systems on which PHAST has been installed.

Restrictions / License Information

Here are the details of the PHAST license.

PHAST LICENSE

-------------
Copyright (c) 2002-2010 University of California, Cornell University
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:

1. Redistributions of source code must retain the above copyright
   notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright
   notice, this list of conditions and the following disclaimer in the
   documentation and/or other materials provided with the distribution.

3. The name of the author may not be used to endorse or promote products
   derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

PCRE LICENSE

------------
PHAST makes use of PCRE, an open-source library that supports perl-like
regular expressions.  Redistribution of PCRE along with PHAST is permitted
under the terms of PCRE's license.  That license is reproduced in its
entirety below.
-----

PCRE is a library of functions to support regular expressions whose syntax
and semantics are as close as possible to those of the Perl 5 language.

Release 8 of PCRE is distributed under the terms of the "BSD" licence, as
specified below. The documentation for PCRE, supplied in the "doc"
directory, is distributed under the same terms as the software itself.

The basic library functions are written in C and are freestanding. Also
included in the distribution is a set of C++ wrapper functions.

THE BASIC LIBRARY FUNCTIONS

---------------------------
Written by:       Philip Hazel
Email local part: ph10
Email domain:     cam.ac.uk
University of Cambridge Computing Service,
Cambridge, England.
Copyright (c) 1997-2010 University of Cambridge
All rights reserved.

 
THE "BSD" LICENCE
-----------------
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:


    * Redistributions of source code must retain the above copyright notice,
      this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above copyright
      notice, this list of conditions and the following disclaimer in the
      documentation and/or other materials provided with the distribution.
 
    * Neither the name of the University of Cambridge nor the name of Google
      Inc. nor the names of their contributors may be used to endorse or
      promote products derived from this software without specific prior
      written permission.


THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.

Running Instructions

Initialize your environment by running the appropriate module command.  See the Software Versions page for the specific commands to use on the WestGrid systems on which PHAST has been installed.

For More Information

2016-09-18 - Added Breezy installation to software versions.

System Breezy Jasper
Version 1.3 1.3