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MAximum Parsimonious Likelihood Estimation in C/C++

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# CMAPLE

[![License (GPL v2.0)](https://img.shields.io/badge/GPL%20v2.0-License?logo=gnu&label=License)](https://opensource.org/license/gpl-2-0)
[![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/cmaple.svg?label=Bioconda%20installs)](https://anaconda.org/bioconda/cmaple)
[![Bioconda platforms](https://img.shields.io/conda/pn/bioconda/cmaple.svg?&label=Bioconda%20platforms)](https://github.com/bioconda/bioconda-recipes/tree/master/recipes/cmaple)

## What's CMAPLE?

CMAPLE is a C++ reimplementation of [MAPLE][MAPLE_FORMAT] - 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 <TBU>**API_Documentation**.

## How to cite CMAPLE?

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](https://doi.org/10.1093/molbev/msae134).

## How to use CMAPLE?

Please refer to our [User-Manual](https://github.com/iqtree/cmaple/wiki/User-Manual) for installation instructions and usage examples of CMAPLE.

## How to compile CMAPLE from source?

For advanced users, if one wants to compile CMAPLE from source code, please refer to our [Compilation Guide](https://github.com/iqtree/cmaple/wiki/Compilation-Guide).

## Contributing - Get Involved!

See [CONTRIBUTING](CONTRIBUTING.md) file.

## Code of Conduct

CMaple is governed by some rules, which serve to protect our community and its individuals. See [CODE_OF_CONDUCT](CODE_OF_CONDUCT.md) for details.

## Acknowledgment
CMAPLE relies on the following third-party libraries:

- **[ncl](https://github.com/mtholder/ncl)** (version 2.0) - Licensed under the [GNU General Public License](https://github.com/mtholder/ncl/blob/master/COPYING).
- **[simde](https://github.com/simd-everywhere/simde)** - Licensed under the [MIT License](https://github.com/simd-everywhere/simde/blob/master/COPYING).
- **[zlib](http://zlib.net/)** (version 1.2.7).

[CMAPLE_RELEASES]: https://github.com/trongnhanuit/cmaple/releases
[Gaston et al. 2011]: https://doi.org/10.1093/bioinformatics/btr470
[MAPLE_FORMAT]: https://www.nature.com/articles/s41588-023-01368-0
[DNA_MODELS]: #dna-models
[AA_MODELS]: #amino-acid-models
[TREE_SEARCH]: #4-set-the-tree-search-type
[Guindon et al., 2010]: https://academic.oup.com/sysbio/article/59/3/307/1702850
[IQ_TREE]: http://www.iqtree.org/
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