PRANK

PRANK performs probabilistic, phylogeny-aware multiple sequence alignment of DNA, codon, and amino acid sequences to improve inference of evolutionary homology.

Key Features:

• Phylogeny-Aware Alignment: Integrates phylogenetic information and a guide phylogeny into the alignment algorithm to inform alignment decisions.
• Handling of Indels: Models insertions and deletions separately and marks gaps distinctly in the output to reflect their different origins.
• Inference of Ancestral Sequences: Infers ancestral sequences as a by-product of the alignment process.
• Sensitivity to Phylogenetic Errors: Alignment accuracy depends on the correctness of the guide phylogeny and assumptions about gap patterns.

Scientific Applications:

• Comparative and Phylogenetic Analyses: Produces alignments that better reflect evolutionary homology for comparative and phylogenetic studies.
• Molecular Evolution Studies: Enables investigation of patterns of insertions, deletions, and sequence evolution at DNA, codon, and amino acid levels.
• Phylogeny Reconstruction: Provides homology-informed alignments to support downstream phylogeny reconstruction.
• Functional Analysis of Sequence Variation: Improves interpretation of functional implications of sequence variation by reducing alignment artifacts.

Methodology:

PRANK applies probabilistic models that incorporate a guide phylogeny to guide the alignment, models insertions and deletions separately, marks gaps distinctly in the output, and infers ancestral sequences.