SWAMP: Sliding Window Alignment Masker for PAML.

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Genome-wide scans for positive selection are increasingly common.
• Different sequencing methods introduce potential errors.
• Sequencing and alignment errors inflate false positive rates in adaptive evolution studies.

Purpose of the Study:

• To introduce a novel tool, SWAMP (Sliding Window Alignment Masker for Phylogenetic Analysis by Maximum Likelihood), for masking erroneous sequence data.
• To enhance the reliability of downstream evolutionary analyses by filtering out problematic sequence regions.

Main Methods:

• SWAMP scans multiple-sequence alignments for regions with high nonsynonymous substitution rates, indicative of errors.
• It masks short stretches of erroneous sequence, especially in low-coverage genomes.
• The tool allows flexible masking strategies based on phylogenetic branch length, divergence, or assembly quality.

Main Results:

• SWAMP effectively masks erroneous sequence data that may be missed by other methods.
• Demonstrated effectiveness on a dataset of 6,379 primate protein-coding genes with variable data quality.
• Reduces false-positive rates in genome-wide analyses.

Conclusions:

• SWAMP improves the reliability of genome-wide evolutionary analyses by filtering sequence errors.
• Its flexible masking approach enhances reproducibility and accuracy.
• Essential for studies using diverse and potentially low-quality genomic data.