MACSE

MACSE aligns protein-coding nucleotide sequences into multiple sequence alignments that preserve amino-acid translation and codon structure for analyses of coding-sequence evolution.

Key Features:

• Alignment of Coding Sequences: Generates multiple sequence alignments that maintain reading frames and respect codon boundaries for protein-coding nucleotide sequences.
• Handling Frameshifts and Stop Codons: Permits and models the presence of frameshift mutations and premature stop codons within alignments to represent both functional genes and pseudogenes.
• Codon Structure Consideration: Preserves codon structure to support downstream codon-based analyses, including studies of nonsynonymous to synonymous substitution ratios.

Scientific Applications:

• Genomic and Evolutionary Analyses: Produces codon-aware MSAs for comparative genomics and evolutionary studies of coding-sequence divergence.
• Pseudogene Analysis: Aligns nonfunctional sequences containing frameshifts and stop codons to facilitate analysis of pseudogene evolution and degeneration.

Methodology:

Aligns coding nucleotide sequences while preserving their amino-acid translation by allowing frameshifts and stop codons within the alignment process so that both functional and nonfunctional sequences are represented.