Aligning Protein-Coding Nucleotide Sequences with MACSE.

Most genomic and evolutionary comparative analyses rely on accurate multiple sequence alignments. With their underlying codon structure, protein-coding nucleotide sequences pose a specific challenge for multiple sequence alignment. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that provided the first automatic solution for aligning protein-coding gene datasets containing both functional and nonfunctional sequences (pseudogenes). Through its unique features, reliable codon alignments can be built in the presence of frameshifts and stop codons suitable for subsequent analysis of selection based on the ratio of nonsynonymous to synonymous substitutions. Here we offer a practical overview and guidelines on the use of MACSE v2. This major update of the initial algorithm now comes with a graphical interface providing user-friendly access to different subprograms to handle multiple alignments of protein-coding sequences. We also present new pipelines based on MACSE v2 subprograms to handle large datasets and distributed as Singularity containers. MACSE and associated pipelines are available at: https://bioweb.supagro.inra.fr/macse/ .