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

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.

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.

Pangenome analysis of eukaryotes.

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

Simulation of the motion of the eukariotic cell Chlamydomonas Reinhardtii

Scripts for paper Vaulot et al. 2022

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

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

Pipeline for eukaryotic genome annotation based on external evidences

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

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.

NextITS pipeline documentation

examination of genome size across all kingdoms

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

tiara – a tool for DNA sequence classification

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

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

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

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