Bioinformatics Tools

MitoFinder

Allio, R., Schomaker‐Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020). MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Molecular Ecology Resources, 20(4), 892-905. DOI: 10.1111/1755-0998.13160

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data. MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data…)

GABBI

Zelvelder, B., Benoit, L., Loiseau, A., Haran, J., & Allio, R. (2026). A new method based on genome alignments provides a highly resolutive target enrichment set for weevils (Coleoptera, Curculionoidea). bioRxiv, 2026-05. DOI: 10.64898/2026.05.09.724036

GABBI is a fully automated pipeline for designing target capture baits (or probes) from whole-genome alignments. Probe sets derived from GABBI are expected to target more variable loci than those produced by conventional probe design methods that rely on a single reference genome for mapping reads, thereby providing more sensitive and phylogenetically informative data.

PhylteR

Comte, A., Tricou, T., Tannier, E., Joseph, J., Siberchicot, A., Penel, S., Allio, R., Delsuc, F., Dray, S., & de Vienne, D. M. (2023). PhylteR: efficient identification of outlier sequences in phylogenomic datasets. Molecular Biology and Evolution, Volume 40, Issue 11, November 2023, msad234. DOI: 10.1093/molbev/msad234

PhylteR is a tool that allows detecting, removing and visualizing outliers in phylogenomics dataset by iteratively removing taxa from gene families (gene trees) and optimizing a score of concordance between individual matrices.

Database

OrthoMaM

Allio, R., Delsuc, F., Belkhir, K., Douzery, E. J., Ranwez, V., & Scornavacca, C. (2023). OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics. Nucleic Acids Research, gkad834. DOI: 10.1093/nar/gkad834

OrthoMaM , a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of coding sequences in mammalian genomes. OrthoMaM version 12 includes 15,868 alignments of orthologous coding sequences (CDS) from the 190 complete mammalian genomes currently available.

Protocols

ONT sequencing

Allio R., Tilak M. K., Scornavacca C., Avenant N. L., Corre E., Nabholz B., & Delsuc F. (2021). High-quality carnivore genomes from roadkill samples enable species delimitation in aardwolf and bat-eared fox. eLife, 10, e63167. DOI: 10.7554/eLife.63167

This protocol was developed to optimize DNA sequencing from mammalian roadkill tissue samples using Oxford Nanopore Technology (ONT).