PRANK API

PRANK API performs probabilistic multiple sequence alignment of DNA, codon, and amino acid sequences to produce phylogeny-aware alignments that distinguish insertions from deletions for evolutionary analyses.

Key Features:

• Probabilistic Framework: Implements a probabilistic model that integrates evolutionary distances and phylogenetic relationships to improve alignment accuracy.
• Insertion vs. Deletion Differentiation: Distinguishes insertions from deletions rather than treating all gaps identically, preventing overestimation of deletions and underestimation of insertions.
• Phylogeny-Aware Alignment: Aligns sequences using phylogenetic information so gaps are attributed in a manner consistent with evolutionary history.
• Ancestral Sequence Inference: Infers ancestral sequences and annotates gaps based on inferred insertion or deletion origin.
• Handling of Evolutionary Hot Spots: Reduces spatial concentration of gaps to avoid artifactual insertion/deletion hotspots in alignments.
• Supported Sequence Types: Handles DNA, codon, and amino acid sequences.
• Pair HMM and Evolutionary Scoring: Utilizes a pair hidden Markov model with an evolutionary scoring function and incorporates elements from maximum likelihood phylogenetic approaches.
• Sensitivity to Guide Phylogeny: Alignment results are sensitive to errors in the guide phylogeny and assumptions about gap origins.

Scientific Applications:

• Phylogenetic inference: Provides alignments that reflect evolutionary homology to support robust phylogenetic tree estimation.
• Comparative evolutionary analyses: Enables comparative analyses of genes and proteins using phylogenetically consistent alignments.
• Ancestral reconstruction: Supports reconstruction of evolutionary history through inferred ancestral sequences and gap-origin annotation.

Methodology:

PRANK modifies traditional alignment methods by using a pair hidden Markov model with an evolutionary scoring function and incorporating elements of maximum likelihood phylogenetic approaches to distinguish insertions and deletions and produce phylogeny-consistent alignments.