SuiteMSA

SuiteMSA evaluates and compares multiple sequence alignments to assess alignment quality and to generate simulated reference MSAs for benchmarking alignment reconstruction methods.

Key Features:

• Direct comparison of multiple MSAs: Compares two or more MSAs and identifies regions of agreement (consistency) and disagreement (inconsistency).
• Alignment statistics: Computes alignment statistics to quantify alignment quality and compare MSA performance.
• Phylogeny editing and visualization: Provides tools for editing and visualizing phylogenetic trees associated with sequence data.
• Sequence evolution simulation: Uses sequence evolution simulation to generate reference MSAs that serve as benchmarks for evaluation.

Scientific Applications:

• Phylogenetic inference: Assess the impact of alignment quality on phylogenetic reconstruction.
• Protein structure prediction: Evaluate MSAs used in homology-based protein structure prediction.
• Functional annotation: Assess alignment reliability for comparative functional annotation.

Methodology:

The methodology uses sequence evolution simulations to create reference MSAs, integrates these references with direct MSA comparison and statistical analysis, and includes phylogenetic visualization.