Hapl-o-Mat is software for haplotype inference via an expectation-maximization algorithm. It supports processing and resolving various forms of HLA genotype data.
The latest version can be found on the Github server under https://github.com/DKMS/Hapl-o-Mat
Installing Hapl-o-Mat requires a C++ compiler with C++11 support. To produce the required data on HLA nomenclature python (version 2 or 3) is required.
Get Hapl-o-Mat via
git clone https://github.com/DKMS/Hapl-o-Mat
Using GNU compiler collection (GCC), Hapl-o-Mat is compiled via a Makefile:
make
make clean
If you use another compiler than GCC, adapt the compiler flags in the Makefile, e.g. -march=native.
A detailed explanation on how to install Hapl-o-Mat under Windows using Visual Studio Code can be found in detailedGettingStartedWindows.pdf.
For information on how to use Hapl-o-Mat and some tutorials using Linux follow the guide detailedGettingStartedLinux.pdf. If you are a seasoned Linux user, refer to gettingStarted. If you use Windows, follow the guide detailedGettingStartedWindows.pdf.
If you use Hapl-o-Mat for your research, please cite
Schäfer C, Schmidt AH, Sauter J. Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data. BMC Bioinformatics. 2017; 18(1):284. doi: 10.1186/s12859-017-1692-y.
If you want to participate in actively developing Hapl-o-Mat please join via Github
Dr. Christian Schäfer
Dr. Jürgen Sauter
DKMS gGmbH
Kressbach 1
72072 Tuebingen, Germany
T +49 7071 943-2060
F +49 7071 943-2090
sauter(at)dkms.de
Copyright (C) 2016, DKMS gGmbH
DKMS gGmbH
Kressbach 1
72072 Tuebingen, Germany
T +49 7071 943-2060
F +49 7071 943-2090
sauter(at)dkms.de
Hapl-o-Mat 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 3, or (at your option) any later version.
Hapl-o-Mat 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 Hapl-o-Mat; see the file COPYING. If not, see http://www.gnu.org/licenses/.