baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.

RNA virus analysis toolkit

Metagenomics-related extended functionalities to samtools

Posit Cheat Sheets - Can also be found at https://posit.co/resources/cheatsheets/.

MetaCRAST: reference-guided CRISPR detection in metagenomes

A NumPy port of the foldseek code for encoding protein structures to 3di.

A Wes Anderson color palette for R

Comprehensive list of color palettes available in R ❤️🧡💛💚💙💜

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Toolkit for processing sequences in FASTA/Q formats

VirBot: a protein-based RNA virus detector for metagenomic data

A proof-of-concept, automated and reproducible pipeline for predicting functional associations between pVOGs.

bedtools - the swiss army knife for genome arithmetic

Phage Annotation using Protein Structures

An community curated awesome list of tools, software, databases and other resources for working/analysing RNA Viruses

A listing of software, tools and databases useful for virome analysis

Bayesian Evolutionary Analysis Sampling Trees

All Algorithms implemented in Python

Phylogenetic orthology inference for comparative genomics

Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5

a command line tool for viral proteomic tree generation, part of the ViPTree project: http://www.genome.jp/viptree

GeneValidator: Identify problems with predicted genes

Convert various sequence formats to FASTA