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

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.

Fig. 1.

The graphical user interface of MACSE v2 (left) allows to select the desired subprogram, to browse the file system for choosing input FASTA files, and to set parameter values. It automatically generates the corresponding command line (bottom left). When the user selects a new subprogram or click on an option field, a brief help related to this program or option is displayed on the top of the interface (red arrows). An exemplar data set of 15 mitochondrial NADH dehydrogenase subunit 3 (nad3) gene sequences of turtles has been aligned by MACSE (parameters shown). The resulting alignment is displayed at the nucleotide (top right), codon (middle), and amino acid (bottom right) levels using SeaView v4.6.4 (Gouy et al.2010). Exclamation marks (!) emphasize the frameshifts detected by MACSE, most of which corresponding to programmed frameshift mutations (Russell and Beckenbach 2008).