Metadata-Version: 2.1
Name: revolutionhtl
Version: 1.0.1
Summary: REvolutionH-tl: Reconstruction of Evolutionary Histories tool
Author-email: José Antonio Ramírez-Rafael <jose.ramirezra@cinvestav.mx>
Project-URL: Homepage, https://gitlab.com/jarr.tecn/revolutionh-tl
Project-URL: Bug Tracker, https://gitlab.com/jarr.tecn/revolutionh-tl/issues
Keywords: Evolution reconstruction,Trees inference,Trees reconciliation,Best match graphs,Orthology
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

![REvolutionH-tl logo.](https://gitlab.com/jarr.tecn/revolutionh-tl/-/raw/master/docs/images/Logo_horizontal.png)

Bioinformatics tool for the reconstruction of evolutionary histories. Input: fasta files or sequence alignment hits, Output: event-labeled gene trees and reconciliations.

[Bioinformatics & complex networks lab](https://ira.cinvestav.mx/ingenieriagenetica/dra-maribel-hernandez-rosales/bioinformatica-y-redes-complejas/)

- José Antonio Ramírez-Rafael [jose.ramirezra@cinvestav.mx]
- Maribel Hernandez-Rosales [maribel.hr@cinvestav.mx ]

# Install

```bash
pip install revolutionh-tl
```

**Requirements**

- [Python >=3.7 ](https://www.python.org/)
- [pip](https://pip.pypa.io/en/stable/installation/)

For sequence alignments using revolutionhtl: [Diamond](https://github.com/bbuchfink/diamond)

# Usage

> Go to the [wiki](https://gitlab.com/jarr.tecn/revolutionh-tl/-/blob/master/docs/wiki.md?ref_type=heads) for details and an [example](https://gitlab.com/jarr.tecn/revolutionh-tl/-/blob/master/docs/example.md?ref_type=heads).

```bash
python -m revolutionhtl <arguments>
```

# Pipeline

1. **Orthogroup & best hit selection.** Input: alignment hits (generate this using `revolutionhtl.diamond`) .
2. **Orthology and gene tree reconstruction.** Input: best hits (generate this at step 1).
3. **Species tree reconstruction.** Input: gene trees (generate this at step 2).
4. **Tree reconciliation.** Input: gene and species trees (generate this at steps 2 and 3).

![pipeline](https://gitlab.com/jarr.tecn/revolutionh-tl/-/raw/master/docs/images/revolution_diagram.png){width=80%}

