Evolution Python Packages

pyglove

Manipulating Python Programs

phykit

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

msasim

Backend C++ code for the Sailfish MSA simulation library using the Pybind11 framework

cogent3

Comparative Genomics Toolkit 3

phylotrackpy

Python phylogeny tracker for in silico evolution experiments

py-ste

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

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.

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

evolutionary-policy-optimization

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

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

hyphlow

A GUI-based bioinformatics pipeline for preparing, running, and summarizing HyPhy evolutionary selection analyses.

x-evolution

Implementation of various evolutionary algorithms, starting with evolutionary strategies

trisicell

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

x-transformers-rl

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

metevolsim

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

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

asymmetree

Simulator for species and gene trees with asymmetric evolution rates

gpmap

A Python API for managing genotype-phenotype map data

darwinio

Evolution Simulator

epistasis

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

fastoma

FastOMA is a scalable software package to infer orthology relationship.

phylo3d-trait

Interactive 3D phylogenetic tree visualizer for continuous trait evolution and supplied ancestral-state estimates; standalone WebGL2 HTML.

phenopype

A phenotyping pipeline for Python