Package to extract Unannotated Regions from prokaryotic genomes report coding and pseudogenised genes delimited by stop codons - Named StORFs (Stop - Open Reading Frames)

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

Tracks Eukaryotic genome annotations (gff) from NCBI and Ensembl

PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees

Hail helper functions for the gnomAD project and Translational Genomics Group

Generative art project using GAs and swarm mechanics curated as part of the Norman Rea Gallery's Virtually Real exhibition.

Repository for the TRANSIT and TPP tools developed by the Ioerger Lab

A selection of databases for Genestrip

Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"

GENA-LM is a transformer masked language model trained on human DNA sequence.

Arche: a functional-optimized annotator for microbial meta(genomes)

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

MAGset is a tool to analyze and compare MAGs of known species

This script uses NCBI's Entrez Programming Utilities to perform searches of NCBI databases. This script can return either the complete database records, or the IDs of the records.

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

Assembled Genomes Compressor

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

R code in R Markdown used for ucm genomes and genome analysis course