MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons. (25th August 2018)

• Record Type: Journal Article
• Authors: Ranwez, Vincent; Douzery, Emmanuel J P; Cambon, Cédric; Chantret, Nathalie; Delsuc, Frédéric
• Editors: Wilke, Claus
• Is Part Of: Molecular biology and evolution. Volume 35:Number 10(2018)
• Page Start: 2582
• Page End: 2584
• Publication Date: 2018-08-25
• Subjects: multiple sequence alignment -- molecular evolution -- phylogenomics -- pseudogenes -- metabarcoding; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msy159
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: 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.