matOptimize

matOptimize optimizes mutation-annotated trees (MATs) by parsimony using subtree pruning and regrafting (SPR) moves to refine phylogenetic tree topology for analysis of rapidly evolving datasets such as SARS-CoV-2.

Key Features:

• Parsimony-Based Optimization: Employs parsimony to minimize inferred evolutionary changes when optimizing mutation-annotated trees (MATs).
• Subtree Pruning and Regrafting (SPR): Performs SPR moves within a user-defined radius to explore alternative topologies and improve tree parsimony.
• Scalability and Efficiency: Implements optimizations that report improvements in runtime and peak memory usage, enabling analysis of large trees containing millions of sequences such as SARS-CoV-2.
• Parallelization Capabilities: Supports parallel execution across multiple CPU threads and nodes to accelerate optimization.
• Online Phylogenetics Support: Allows incremental addition of samples to a growing phylogeny to support online phylogenetics workflows during ongoing outbreaks.

Scientific Applications:

• Large-scale SARS-CoV-2 phylogeny maintenance: Refining and maintaining daily large-scale SARS-CoV-2 phylogenies.
• Viral evolution and transmission dynamics: Supporting analyses of viral evolution and transmission dynamics via parsimonious tree optimization.
• Real-time outbreak phylogenetics: Enabling real-time phylogenetic analysis during ongoing outbreaks through incremental sample addition.

Methodology:

Optimizes mutation-annotated trees (MATs) using parsimony and subtree pruning and regrafting (SPR) moves within user-specified radii, with support for parallel execution across CPU threads and nodes and incremental addition of samples.