Evolution Python Packages

pyglove

Manipulating Python Programs

cogent3

Comparative Genomics Toolkit 3

phylotrackpy

Python phylogeny tracker for in silico evolution experiments

phykit

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

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

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.

pioreactor

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

x-transformers-rl

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

py-ste

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

neocoder

neoCoder - AI-Native Engineering Agent for Enterprise-Scale Codebase

evolutionary-policy-optimization

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

trisicell

No description available

x-evolution

x-evolution

oppoppopinit

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

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

jlsteenwyk-biokit

No description available

metevolsim

MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.

adaad

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

asymmetree

Simulator for species and gene trees with asymmetric evolution rates

phenopype

A phenotyping pipeline for Python

opqua

Epidemiological modeling framework for pathogen population genetics and evolution.

darwinio

Evolution Simulator

fastoma

FastOMA is a scalable software package to infer orthology relationship.

gpmap

A Python API for managing genotype-phenotype map data