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

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

Scripts for paper Vaulot et al. 2022

NextITS pipeline documentation

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

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

Datasets and statistics code used for "Objective 1" for PhD Thesis

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.

Sequence processing and analysis code used to investigate the effects of different DNA extraction methods and PCR variability on multi-taxon DNA meta-barcoding estimates of soil biodiversity.

Simulation of the motion of the eukariotic cell Chlamydomonas Reinhardtii

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

Pipeline for eukaryotic genome annotation based on external evidences

examination of genome size across all kingdoms

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

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.

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

Pangenome analysis of eukaryotes.

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

tiara – a tool for DNA sequence classification