Evolution Python Packages

pyglove

Manipulating Python Programs

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

cogent3

Comparative Genomics Toolkit 3

phykit

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

x-transformers-rl

Implementation of a transformer for reinforcement learning using `x-transformers`

phylotrackpy

Python phylogeny tracker for in silico evolution experiments

evolutionary-policy-optimization

Pytorch implementation of Evolutionary Policy Optimization, from Wang et al. of the Robotics Institute at Carnegie Mellon University

magicsoup

MagicSoup is a game that simulates cell metabolic and transduction pathway evolution. Define a 2D world with certain molecules and reactions. Add a few cells and create evolutionary pressure by selectively replicating and killing them. Then run and see what random mutations can do.

py-ste

A Python package for evolving unitaries and states under the Schrödinger equation using first-order Suzuki-Trotter and computing switching functions.

pioreactor

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

oppoppopinit

PyPI package containing opposition learning operators and population initializers for evolutionary algorithms

trisicell

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

x-evolution

Implementation of various evolutionary algorithms, starting with evolutionary strategies

adaad

ADAAD — Autonomous Device-Anchored Adaptive Development. Full local AI ecosystem (Beast Mode, Dream Mode, Cryovant, Aponi Dashboard).

metevolsim

MetEvolSim (Metabolome Evolution Simulator) Python Package

asymmetree

Simulator for species and gene trees with asymmetric evolution rates

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

pyasr

Ancestral Sequence Reconstruction in Python

neocoder

AI Agent | AI Coding Agent | Agent Swarm | AI-Native Engineering Agent for Enterprise-Scale Codebase

opqua

Epidemiological modeling framework for pathogen population genetics and evolution.

gpmap

A Python API for managing genotype-phenotype map data

darwinio

Evolution Simulator

jlsteenwyk-biokit

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

fastoma

FastOMA is a scalable software package to infer orthology relationship.