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
- Create a YAML configuration file defining fixed and optimized parameters.
- Run the parameter optimization with:
itrails-optimize config.yaml --input path/to/alignment.maf --output path/to/output/output_prefix
- 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
1 maintainer
Release files for itrails 2.0.6
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| itrails-2.0.6.tar.gz | 102.6 kB | Details |
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| itrails-2.0.6-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 224.0 kB
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