README

This is profuse, a suite of programs for working with Profile HMMs.
Please see the document CITING, which should have been included with
this file.  You may use at will, subject to the license (GPL v2),
but *please cite the relevant papers* in your documentation and
publications associated with uses of this library.  Thank you!

Copyright (C) 2015 by Paul T Edlefsen, Fred Hutchinson Cancer Research
Center.

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 2 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

-----
PLATFORMS:

Although profuse has been designed for cross-platform use, the
current version has only been tested on Mac OS X systems.  It should
easily install on any other *nix platform.  If you are on Windows, and
want to compile this, we recommend using Cygwin.  If you are able to
compile this on Windows or elsewhere, please let us know and tell us
what you did to make it happen.  Thanks.

DEPENDENCIES:

profuse relies on a number of other libraries.  All are open source
and are easy to install.

Required external libraries:
---
BOOST (tested with version 1.59.0)
Seqan (direct from github)

HMMoC-BFloat-Algebra:
https://github.com/pedlefsen/HMMoC-BFloat-Algebra

Required galosh libraries:
---
prolific (NOT the same thing as "profillic"):  https://github.com/galosh/prolific

Recommended galosh libraries:
---
profillic:  https://github.com/galosh/profillic

See the document INSTALL for more information.

Thank you,
  Paul

Paul T. Edlefsen
October 23, 2015