Historian

Historian reconstructs ancestral sequences and estimates evolutionary parameters, including insertion-deletion (indel) rates, using explicit evolutionary models.

Key Features:

• ProtPal reimplementation and heuristics: Reimplements the ProtPal algorithm and integrates performance-enhancing heuristics from other alignment tools to improve computational efficiency.
• Explicit evolutionary models and alignment uncertainty: Uses explicit evolutionary models that sum over uncertain alignments to account for alignment ambiguity during ancestral reconstruction and rate estimation.
• Evaluation on benchmarks: Evaluated by simulation benchmarks focused on rate estimation fidelity and by the structurally informed alignment dataset BAliBase 3.0, reporting improved accuracy and performance compared to other tools.

Scientific Applications:

• Ancestral Sequence Reconstruction: Reconstruction of ancestral sequences from extant species to infer evolutionary changes.
• Estimation of Evolutionary Rates: Estimation of parameters such as indel rates to analyze molecular evolution dynamics for phylogenetics, comparative genomics, and evolutionary biology.

Methodology:

Reimplements the ProtPal algorithm, incorporates performance-enhancing heuristics from other alignment tools, and employs explicit evolutionary models that sum over uncertain alignments.