Metadata-Version: 2.4
Name: itrails
Version: 2.0.2
Summary: Tree reconstruction of ancestry using incomplete lineage sorting
Author-email: Iker Rivas-González <iker_rivas_gonzalez@eva.mpg.de>, David Martin-Pestana <dmape@birc.au.dk>
Maintainer-email: David Martin-Pestana <dmape@birc.au.dk>
License: MIT License
        
        Copyright (c) 2025 Iker Rivas-González & David Martin-Pestana
        
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Project-URL: Homepage, https://github.com/trails-phylogeny/itrails
Project-URL: BugTracker, https://github.com/trails-phylogeny/itrails/issues
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy==1.26.4
Requires-Dist: scipy==1.13.0
Requires-Dist: joblib==1.4.2
Requires-Dist: numba==0.59.1
Requires-Dist: biopython==1.84
Requires-Dist: pyyaml==6.0.2
Requires-Dist: h5py
Requires-Dist: pandas
Requires-Dist: ray[default]
Provides-Extra: docs
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Dynamic: license-file

# iTRAILS

iTRAILS is a command-line tool designed to infer population parameters and reconstruct evolutionary histories from genomic data using a coalescent hidden Markov model framework. It offers functionalities such as parameter optimization, Viterbi decoding, and posterior decoding, all wrapped in a user-friendly interface.

## Features

- **Parameter Optimization:** Optimize critical population parameters from genomic alignment data.
- **Gene Tree Decoding:** Infer gene tree topologies across the genome using Viterbi and posterior decoding.
- **Command Line Interface (CLI):** Easily integrate iTRAILS into your bioinformatics workflows.
- **Config File Support:** Customize parameters via YAML configuration files without altering the source code.

## Installation

Install iTRAILS using PyPi:

```bash
pip install itrails
```
Or with conda:
```bash
conda install conda-forge::itrails
```
## Quick Start

1. Create a YAML configuration file defining fixed and optimized parameters.
2. Run the parameter optimization with:

```bash
itrails-optimize config.yaml --input path/to/alignment.maf --output path/to/output/output_prefix
```

3. Run the parameter optimization with: Use the generated Best Model configuration file to perform gene tree decoding with:
  - Viterbi Decoding: ```itrails-viterbi```
  - Posterior Decoding: ```itrails-posterior```

## Documentation

For more detailed instructions, usage examples, and API references, please visit our full documentation at:
[Read The Docs - iTRAILS](https://itrails.readthedocs.io/en/)
