ProPIP is a Multiple Sequence Alignment inference software that implements the Poisson Indel Process (Bouchard-Côté & Jordan, PNAS, 2013) in the Maximum Likelihood framework.
You can find tutorial, examples and guides on our Wikipages
* ProPIP is a computer program whose purpose is to infer Multiple Sequence
* Alignment under an indel-aware model for nucleotide and protein datasets.
*
* This software is based and extends the following libraries:
*
* - the Bio++ libraries
* developed by the Bio++ Development Team <http://biopp.univ-montp2.fr>
*
* - The Tree Search Heuristic Library (TSH-LIB)
* developed by L. Gatti & M. Maiolo <http://bit.ly/tsh-lib>
*
* ProPIP 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.
*
* ProPIP is a free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* You should have received a copy of the GNU Lesser General Public
* License along with ProPIP. If not, see <http://www.gnu.org/licenses/>.[1] Alexandre Bouchard-Côté and Michael I. Jordan. Evolutionary inference via the Poisson Indel Process.Proc. Natl. Acad. Sci. U.S.A., 110(4):1160, 2013.
In case of bugs or improvement suggestions feel free to:
Write to Lorenzo Gatti
Write to Massimo Maiolo