MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

tiara – a tool for DNA sequence classification

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

Pangenome analysis of eukaryotes.

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

Pipeline for eukaryotic genome annotation based on external evidences

A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio

Scripts for paper Vaulot et al. 2022

examination of genome size across all kingdoms

Simulation of the motion of the eukariotic cell Chlamydomonas Reinhardtii

SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries

The Tree of Sex Ontology (TOSO) covers any trait related to reproduction included in the Tree of Sex database

This is a microbial amplicon sequence (16S and 18S iTag) data and analyses pipeline corresponding to the manuscript, "Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California" for public benefit and usage.

A library to get information on organisms and UniProt identifiers. This includes growth temperature, growth ph, pfam domains, taxonomic lineage.

MegaVir is a bioinformatic pipeline for virome characterization and genome assembly.

V. M. Gumerov, E. P. Andrianova, M. A. Matilla, Karen M. Page, Elizabet Monteagudo-Cascales, A. C. Dolphin, T. Krell, I. B. Zhulin (2022). Amino acid sensor conserved from bacteria to humans.

EuCAP, a Eukaryotic Community Annotation Package (adapted from the implementation developed for the Rice Genome Annotation Project)

A program that uses the Synteny Index algorithm to compare between Eukaryotes.