ALIFRITZ

ALIFRITZ performs simultaneous statistical multiple sequence alignment and phylogeny reconstruction by integrating indel-aware models (including TKF2) and a simulated annealing optimization to infer alignments, indel histories, and phylogenetic trees from DNA or protein sequences.

Key Features:

• Simulated Annealing Strategy: Employs a simulated annealing algorithm to explore alignment and phylogenetic-tree space and facilitate convergence to improved solutions.
• Indel History Integration: Incorporates indel models to augment multiple alignments with explicit positioning of insertion and deletion events within the phylogenetic tree.
• TKF2 Model Application: Applies the TKF2 probabilistic model to account for the stochastic nature of insertions and deletions during alignment and tree inference.

Scientific Applications:

• Phylogenetic Analysis: Reconstructs phylogenetic trees alongside sequence alignments for DNA or protein datasets to assess evolutionary relationships.
• Evolutionary Biology Research: Traces indel histories to investigate mechanisms of molecular evolution and sources of genetic variation.
• Method Validation and Empirical Illustration: Methodology validated through simulations and illustrated using a primate mitochondrial DNA (mtDNA) dataset.

Methodology:

Accepts DNA or protein sequences as input, applies a simulated annealing-based iterative strategy to jointly refine multiple sequence alignments and phylogenetic trees, and incorporates indel models including TKF2 to position insertion and deletion events and model stochastic indel processes.