mothur

DeepTaxa is a hybrid CNN-BERT deep learning framework for multi-rank taxonomic classification of 16S rRNA gene sequences. It predicts all seven Linnaean ranks from domain to species in a single forward pass and provides pre-trained checkpoints for full-length 16S and V3-V4 amplicons.

Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.

Toolkit for processing sequences in FASTA/Q formats.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Vision foundation model for the tree of life, pretrained on diverse biological imagery across taxa for zero-shot species identification, trait extraction, and biodiversity research (Ohio State University Imageomics Institute)