Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

fast phage annotation program

Phage Annotation using Protein Structures

High accuracy RAG for answering questions from scientific documents with citations

BWT construction and search

LexicMap: efficient sequence alignment against millions of prokaryotic genomes

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.

a short-read polishing tool for long-read assemblies

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Pairwise whole genome aligner

ATLAS - Three commands to start analyzing your metagenome data

Tool for fully-automated inference of species trees from raw genome assemblies

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

tiara – a tool for DNA sequence classification

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

Microbiome classification pipeline

Classify metagenomic contigs as eukaryotic or prokaryotic

Eukfinder: A pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and …

Automatically exported from code.google.com/p/cdhit

PSAURON is a machine learning model for rapid assessment of protein coding gene annotation

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

alignment-free coverage calculation for metagenomic binning >100 times faster

Automated taxonomy decoration onto a tree

Processing support for Greengenes2

geNomad: Identification of mobile genetic elements

Python packaging and dependency management made easy

🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies

CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes