PEPR - Phylogenomic Estimation with Progressive Refinement

Examples

Two example data sets are provided in the examples/ directory. These are to verify 
that your installation is working, and to provide example commands you can modify 
to begin building your own trees. 

To run the Erysipelotrichales example, run the following commands from the 'pepr'
directory containing this README document:

cd examples/
mkdir run_erysipelotrichales
cd run_erysipelotrichales/
sh ../../dist/pepr/scripts/pepr.sh -run_name erysipelotrichales -genome_file \
../Erysipelotrichales/*faa -outgroup ../Erysipelotrichales/outgroup/*faa \
-outgroup_count 2 > erysipelotrichales.out

The Erysipelotrichales example should produce a tree with 100% support for all 
branches on the first round.


To run the Aquificales example, run the following commands:

cd examples/
mkdir run_aquificales
cd run_aquificales/
sh ../../dist/pepr/scripts/pepr.sh -run_name aquificales -genome_file \
../Aquificales/*faa -outgroup ../Aquificales/outgroup/*faa \
-outgroup_count 2 > aquificales.out

The Aquificales example should build a full tree then do one refinement round. The 
resulting tree should have all 100% branch supports, except one branch with ~40%.


PEPR uses several third-party tools, which are included with this distribution for the 
convenience of the end user. PEPR has been tested with these specific versions of these
tools. Other versions may be substituted, but there is no guarantee that PEPR will work
properly with different versions. It is our best understanding that all of these
programs are available under terms that allow them to be distributed in this manner.
This document lists the third-party programs included, and the reasons we believe it is
acceptable for them to be redistributed in this fashion. PEPR itself, as distinct from 
the tools listed below, is released under the terms of the GNU Lesser General Public
License v3, a copy of which is included in the directory containing this README document.

With the exception of FastTree, all third-party tools are unaltered. FastTree was 
modified, with assistance from its author, Morgan Price, in order to use the WAG 
likelihood matrix, rather than the default JTT matrix.

Note that blat is only available for "personal, academic, and non-profit use". If your 
use does not fit this description, you must use the blast option, rather than the blat 
option.

FastTree
        http://www.microbesonline.org/fasttree/ - “FastTree is open source software -- 
        you are free to modify and redistribute it as you wish.”

Gblocks
        http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html “The 
        program is available free of charge for Mac OS X, Windows, Linux and some UNIX 
        systems.

        The software and its accompanying documentation are provided as is, without 
        guarantee of support or maintenance.”

        No restrictions on use or distribution are mentioned.

blastall, formatdb
        “Public Domain Notice” included with the software from NCBI. This notice 
        includes the statements,
        “This software/database is freely available to the public for use. The National 
        Library of Medicine and the U.S. Government have not placed any restriction on 
        its use or reproduction.”

blat
        README file with the blat source code says,
        “All files are copyrighted, but license is hereby granted for personal, 
        academic, and non-profit use. ”

hmmbuild, hmmsearch
        ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/Userguide.pdf
        “HMMER is licensed and freely distributed under the GNU General Public License 
        version 3 (GPLv3). For a copy of the License, see 
        http://www.gnu.org/licenses/.”

mcl
        http://micans.org/mcl/
        “The software is licensed under the GNU General Public License, version 3.”
        http://www.gnu.org/licenses/gpl.txt

muscle
        http://www.drive5.com/muscle/manual/license.html
        “The MUSCLE software, including object and source code and documentation, is 
        donated to the public domain. You may therefore freely copy it for any legal 
        purpose you wish. Acknowledgement of authorship and citation in publications is
        appreciated.”

raxmlHPC, raxmlHPC-PTHREADS
        https://github.com/stamatak/standard-RAxML/blob/master/manual/NewManual.pdf
        “RAxML is open source under GNU GPL”