Metadata-Version: 2.1
Name: PyMutSpec
Version: 0.0.7
Summary: Mutational spectra analysis package
Home-page: https://github.com/mitoclub/PyMutSpec
Author: kpotoh
Author-email: kpotoh <axepon@mail.ru>
License: MIT
Project-URL: Homepage, https://github.com/mitoclub/PyMutSpec
Project-URL: Bug Tracker, https://github.com/mitoclub/PyMutSpec/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy ~=1.22.2
Requires-Dist: pandas ~=1.4.0
Requires-Dist: matplotlib ~=3.5.1
Requires-Dist: seaborn ~=0.11.2
Requires-Dist: biopython ~=1.79
Requires-Dist: ete3 ~=3.1.2
Requires-Dist: tqdm ~=4.62.3
Requires-Dist: PyYAML ~=6.0
Requires-Dist: pytest ~=7.1.2
Requires-Dist: click ~=8.1.3

# PyMutSpec

Python library for mutational spectra analysis

<!-- Calculate mutational spectra using ancestral states from phylogenetic tree -->

## Install

- python 3.8+

Install python venv (optionally)

```bash
python3 -m venv env_spectra
source env_spectra/bin/activate
# pip install -r requirements.txt
python3 setup.py install
```

### Installing newick-utils-1.6

```bash
wget http://bioinfodbs.kantiana.ru/newick-utils-1.6.tar.gz
tar -xvzf newick-utils-1.6.tar.gz
cd newick-utils-1.6
./configure --prefix=/opt/newick-utils-1.6
make install
cd build/bin
ls
```

## References

1. [Iqtree](http://www.iqtree.org/) - efficient software for phylogenomic inference
2. [Genetic codes](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=tgencodes#SG1)
