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MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons
Vincent Ranwez1, Emmanuel J P Douzery2, Cédric Cambon1,2
1AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
Molecular Biology and Evolution
|August 31, 2018
Summary
Multiple sequence alignment is crucial for evolutionary studies. MACSE v2 improves codon alignment accuracy, even with frameshifts, aiding evolutionary analyses.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Biology
Background:
- Multiple sequence alignment is fundamental for evolutionary analyses.
- Existing tools may struggle with codon structure and frameshifts in nucleotide sequences.
Purpose of the Study:
- Introduce MACSE v2, an updated program for multiple alignment of coding sequences (MACSE).
- Enhance the reliability of codon alignments, particularly in the presence of frameshifts.
- Provide a comprehensive toolkit for handling protein-coding sequence alignments.
Main Methods:
- Improved algorithm for multiple sequence alignment of coding sequences.
- Explicitly accounts for codon structure and frameshifts.
- Incorporates a graphical user interface for enhanced usability.
Main Results:
- MACSE v2 generates reliable codon alignments, even with frameshifts.
- Facilitates downstream evolutionary analyses, such as selection pressure estimation.
- Offers a user-friendly toolkit for managing protein-coding sequence alignments.
Conclusions:
- MACSE v2 represents a significant advancement in aligning coding sequences.
- The updated software improves accuracy and accessibility for evolutionary biologists.
- Enables more robust downstream analyses of molecular evolution.
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