CMAPLE is a C++ reimplementation of MAPLE - a novel likelihood-based phylogenetic inference method for pandemic-scale epidemiological genomic data. CMAPLE is highly optimized for performance and scalability with many new features.
Apart from a standalone software, we also provide a set of APIs, which allow users to integrate CMAPLE into existing phylogenetic inference methods. For more detail, please see API_Documentation.
Nhan Ly-Trong, Chris Bielow, Nicola De Maio, Bui Quang Minh, "CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era", Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae134, https://doi.org/10.1093/molbev/msae134.
Please refer to our User-Manual for installation instructions and usage examples of CMAPLE.
For advanced users, if one wants to compile CMAPLE from source code, please refer to our Compilation Guide.
See CONTRIBUTING file.
CMaple is governed by some rules, which serve to protect our community and its individuals. See CODE_OF_CONDUCT for details.
CMAPLE relies on the following third-party libraries:
- ncl (version 2.0) - Licensed under the GNU General Public License.
- simde - Licensed under the MIT License.
- zlib (version 1.2.7).