Metadata-Version: 2.3
Name: pysegul
Version: 0.4.1
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Rust
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Dist: pytest <5.0.0 ; extra == 'test'
Requires-Dist: pytest-cov[all] ; extra == 'test'
Provides-Extra: test
License-File: LICENSE
Summary: Python bindings for the SEGUL high-performance and memory-efficient phylogenomic tools.
Keywords: phylogenomics,bioinformatics,phylogenetics,alignment,SEGUL
Author-email: Heru Handika <hhandi1@lsu.edu>, "Jacob A. Esselstyn" <esselstyn@lsu.edu>
Requires-Python: >=3.8
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: homepage, https://www.segul.app/
Project-URL: documentation, https://www.segul.app/docs/api-usage/python-api
Project-URL: repository, https://github.com/hhandika/pysegul
Project-URL: changelog, https://github.com/hhandika/pysegul/blob/main/CHANGELOG.md

# PySEGUL

![Test](https://github.com/hhandika/pysegul/workflows/ci/badge.svg)
[![PyPI version](https://badge.fury.io/py/pysegul.svg)](https://badge.fury.io/py/pysegul)
![PyPI - Downloads](https://img.shields.io/pypi/dm/pysegul)

PySEGUL is a python bindings of the [SEGUL](https://segul.app) high-performance and memory-efficient phylogenomic tools. It is well-suited for large-scale phylogenomic projects involving thousands of loci, but it is just as capable of handling small Sanger sequences effectively.

Learn more on using PySEGUL in the [documentation](https://www.segul.app/docs/api-usage/python/intro).

## Quick Start

```bash
pip install pysegul
```

To concatenate alignments:

```python
import pysegul

def concat_alignments():
    input_dir = 'tests/concat'
    input_format = 'nexus'
    datatype = 'dna'
    output_format = 'fasta'
    partition_format = 'raxml'
    prefix = 'concatenated'
    output_dir = 'results/concat'
    concat = pysegul.AlignmentConcatenation(
        input_format,  
        datatype, 
        output_dir, 
        output_format, 
        partition_format, 
        prefix
        )
    concat.from_dir(input_dir)

if __name__ == '__main__':
    concat_alignments()
```

