Evolution Python Packages

pyglove

Manipulating Python Programs

cogent3

Comparative Genomics Toolkit 3

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

phykit

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

phylotrackpy

Python phylogeny tracker for in silico evolution experiments

x-transformers-rl

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

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.

pioreactor

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

x-evolution

Implementation of various evolutionary algorithms, starting with evolutionary strategies

trisicell

No description available

oppoppopinit

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

metevolsim

MetEvolSim (Metabolome Evolution Simulator) Python Package

py-ste

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

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.

neocoder

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

asymmetree

Simulation of phylogenetic trees, sequences and genomes

darwinio

Evolution Simulator

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

adaad

ADAAD — Autonomous Development & Adaptation Architecture: governance-first constitutional AI evolution runtime

phenopype

A phenotyping pipeline for python

opqua

An epidemiological modeling framework for population genetics and evolution.

gpmap

A Python API for managing genotype-phenotype map data