Manipulating Python Programs

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.

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

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

Comparative Genomics Toolkit 3

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

Tiny Genetic Programming in Python.

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

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

FastOMA is a scalable software package to infer orthology relationship.

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Algorithm For Gene Order Reconstruction in Ancestors

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

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

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

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

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

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

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

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