Manipulating Python Programs
Comparative Genomics Toolkit 3
Implementation of various evolutionary algorithms, starting with evolutionary strategies
Modular framework for evolutionary algorithms and neuroevolution
An in vivo PRA reveals intronic motifs that combinatorially regulate splicing in a tissue-biased manner.
A phylogeny-aware toolkit for classifying and annotating Hierarchical Orthologous Groups (HOGs) in pangenomic datasets. It's a flexible command-line toolkit for classifying HOGs across multiple genomes in a pangenome-aware, phylogeny-informed context.
Evolution simulator in a physically realistic 2D environment
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
Knowledge-based Identification of Pathway Enzymes (KIPEs) performs an automatic annotation of the flavonoid biosynthesis steps in a new transcriptome of genome sequence assembly.
This is a genetic evolution simulator focused on single-celled organisms called Doplings!
A Python package for evolving states and unitaries under the Schrödinger equation using first-order Suzuki-Trotter and computing switching functions.
A Python package for evolving unitaries and states under the Schrödinger equation using first-order Suzuki-Trotter and computing switching functions.
Genopixel: an artificial ecosystem where bots can compete to get food, try to survive and reproduce
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
a tool to predict highly similar duplicates (HSDs) in eukaryotes
Simulation of an evolving ecosystem with Perlin noise for world generation
RetroSeek is a parallelized, end-to-end computational pipeline designed to detect, categorize and annotate specified ERV integrations in genome assemblies. Built upon the Snakemake workflow management system, it is designed with a strong emphasis on parallelization, modularity, resilience, and reproducibility.
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