itrails 2.0.0

Tree reconstruction of ancestry using incomplete lineage sorting

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:

pip install itrails

Or with conda:

conda install conda-forge::itrails

Quick Start

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

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