MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons
Open accessAbstract
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.
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For the 488 placental mammal and 501 bird assemblies, the paper provides comparative gene annotations, ortholog sets, lists of inactivated genes and multiple codon alignments generated with MACSE v2.
“For the 488 placental mammal and 501 bird assemblies, we provide comparative gene annotations, ortholog sets, lists of inactivated genes and multiple codon alignments generated with MACSE v2 (33) for download at http://genome.senckenberg.de/download/TOGA/.”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [33]
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Vision-related convergent gene losses reveal SERPINE3’s unknown role in the eye
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- Authors
- Ranwez, V., Douzery, E. J. P., Cambon, C., Chantret, N., & Delsuc, F.
- Affiliations
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Ranwez, Vincent
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-08-25
- Volume
- 35
- Issue
- 10
- Pages
- 2582-2584
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC6188553
- OpenAlex
- W2888308804
- Cited by
- 743
- References
- 1
- Citations by year
- 2026: 206 · 2025: 138 · 2024: 143 · 2023: 84 · 2022: 69 · 2021: 56 · 2020: 35 · 2019: 11 · 2018: 1
- FWCI
- 8.99
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by-nc)
- Funders
- Agence Nationale de la Recherche “Investissements d’avenir/Bioinformatique” (ANR-10-BINF-01-02)
- Labex CeMEB “Centre Méditerranéen de l’Environnement et de la Biodiversité” (ANR-10-LABX-0004)
- European Research Council (ERC-2015-CoG-683257)
- Institut des Sciences de l’Evolution de Montpellier
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- multiple sequence alignment, protein-coding sequences, codon alignment, frameshift mutation, stop codon, nonsynonymous substitutions, synonymous substitutions, selection pressure, graphical user interface
- MeSH terms
- Software, Frameshift Mutation, Sequence Alignment, Codon, Terminator
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