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

By Vincent Ranwez, Emmanuel J. P. Douzery, Cédric Cambon, N. Chantret, Frédéric Delsuc. Molecular biology and evolution, 2018

612 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a5c2d0060f37eff231825da53b830595c3fcf764

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Citations in the corpus

• PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies (2019, methodology): “…alignment (MSA) method (Zhu, Li, Salah, Shi, & Li, 2015); due to its comparative advantages ( and then translated back into nucleotides. mafft is also not able to handle sequences with sequencing errors or frameshifts, which can seriously affect the downstream analyses (Ranwez et al., 2018).”