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README
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README
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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”