Manipulating Python Programs
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.
Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** /~https://github.com/heche-psb/wgd.
Algorithm For Gene Order Reconstruction in Ancestors
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
FastOMA is a scalable software package to infer orthology relationship.
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
Outplay the AI with your intelligence
Guided synteny alignment between duplicated genomes (within specified quota constraint)
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Supported highly optimized and flexible genetic algorithm package for python3.8+
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
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