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R package to be released in Bioconductor v3.16 for the assessment of microbiota stability across longitudinal samples
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
A fast whole-genome aligner based on de Bruijn graphs
sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
PANgenome with Annotations, COre identification, Tree and corresponding Alignments
Official home of genome aligner based upon notion of Cactus graphs
👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
A scalable high-throughput metabolic and biogeochemical functional trait profiler
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted stru…
Open source code for CRISPRimmunity
CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
An integrated database for improving taxonomic classification of 16S Ribosomal RNA sequences.
A python library for predicting phage lifestyle based on genome sequence
Predict prokaryotic host for phage metagenomic sequences
Predict prokaryotic hosts for phage (meta) genomic sequences
VirHostMatcher-Net: A network-based computational tool for predicting virus-host interactions.
VirHostMatcher: matching hosts of viruses based on oligonucleotide frequency (ONF) comparison
Visualising data frames as funky heatmaps 📊
Program for estimating dN/dS in overlapping genes (OLGs)
Base for the Viral Genomics and Bioinformatics Repository
Review article on overlapping reading frames in viruses