spartaabc 0.5.5

Indel model parameter inference.

SpartaABC

A Python package for inferring indel (insertion-deletion) model parameters using Approximate Bayesian Computation (ABC).

Description

spartaabc implements ABC methods to estimate parameters of indel models from observed data. This approach is particularly useful when dealing with complex evolutionary models where traditional likelihood-based methods may be computationally intractable.

Installation

You can install spartaabc directly from PyPI:

pip install spartaabc

Quick Start

Here's a basic example of how to use spartaabc:

sparta -i /path/to/data/dir -t AA -n 10000 -nc 100 -s 42

Arguments:

• -i: Input directory containing phylogenetic tree in newick format, and raxml ".bestModel" file.
• -t: Sequence type (AA for amino acid or NT for nucleotide)
• -n: Number of simulations (10000)
• -nc: Number of corrective simulations (100)
• -s: Random number seed (42)

License

This project is licensed under the Academic Free License v3.0.

Contact

• GitHub Issues: Create an issue
• Email: [e-mail]