PSAR

PSAR refines multiple sequence alignments (MSAs) by probabilistic sampling and realignment to improve alignment accuracy for evolutionary and comparative genomic analyses.

Key Features:

• Probabilistic Sampling: Generates suboptimal alignments via probabilistic sampling to explore alternative alignment hypotheses beyond a single optimal MSA.
• Realignment Capability: Refines input MSAs by leveraging the diverse set of sampled suboptimal alignments to correct errors and enhance alignment quality.
• Compatibility with Existing MSA Tools: Accepts MSAs produced by other multiple sequence alignment tools and uses them as inputs for sampling and realignment.

Scientific Applications:

• Evolutionary Biology: Improves MSAs used to infer phylogenetic relationships and evolutionary conservation.
• Genomics: Enhances alignment accuracy for genomic analyses including detection of coding exons and non-coding regulatory sequences.
• Comparative Genomics and Cross-Species Conservation: Refines alignments to increase reliability in identifying conserved regions across species.

Methodology:

Generates a range of suboptimal alignments through probabilistic sampling and then realigns input MSAs using those sampled alignments to produce a refined final alignment.