MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

Vincent Ranwez (1) , Emmanuel J.P. Douzery (2) , Cédric Cambon (1) , Nathalie N. Chantret (1) , Frédéric Delsuc (2)

1 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
2 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier

Multiple sequence alignment is a prerequisite for many evolutionary analyses. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates downstream analyses such as selection pressure estimation based on the ratio of nonsynonymous to synonymous substitutions. Here, we present MACSE v2, a major update with an improved version of the initial algorithm enriched with a complete toolkit to handle multiple alignments of protein-coding sequences. A graphical interface now provides user-friendly access to the different subprograms.

Mots clés: metabarcoding; pseudogenes; phylogenomics; multiple sequence alignment; molecular evolution

Domaines: Sciences du Vivant [q-bio]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Evolution [q-bio.PE]; Systématique, phylogénie et taxonomie

Vincent Ranwez, Emmanuel J.P. Douzery, Cédric Cambon, Nathalie N. Chantret, Frédéric Delsuc. MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons. Molecular Biology and Evolution, 2018, 35 (10), pp.2582 - 2584. ⟨10.1093/molbev/msy159⟩. ⟨hal-01925698⟩