Comparative Genomics Toolkit 3

Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.

Tiny Genetic Programming in Python.

Your toolkit for autonomous, evolving agent ecosystems. Create, execute, govern, and evolve agents that learn from experience, collaborate, build new capabilities, and operate safely within defined guardrails.

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

Manipulating Python Programs

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Python simulation of a single-celled organism

An interesting display of evolution through neural networks and a genetic algorithm

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)

FastOMA is a scalable software package to infer orthology relationship.

A public python implementation of the DeepHyperNEAT system for evolving neural networks. Developed by Felix Sosa and Kenneth Stanley. See paper here: https://eplex.cs.ucf.edu/papers/sosa_ugrad_report18.pdf

Algorithm For Gene Order Reconstruction in Ancestors

Supported highly optimized and flexible genetic algorithm package for python3.8+

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

Pinpoints the mutation favored by selection

A Python API for managing phylogenetics projects

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

a versatile toolkit for processing and analyzing diverse types of sequence data