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Area of Science:

  • Computational Biology
  • Phylogenetics
  • High-Performance Computing

Background:

  • Phylogenetic inference is computationally intensive, benefiting from parallelization.
  • TNT, a parsimony-based phylogenetic program, offers parallelization via the Parallel Virtual Machine (PVM) system.
  • PVM is deprecated, and TNT's parallelization aspects are largely unpublished, limiting its use.

Purpose of the Study:

  • To describe the implementation of parallelization in TNT.
  • To port TNT's parallelization interface to the Message Passing Interface (MPI).
  • To facilitate the use of TNT's parallel analysis capabilities.

Main Methods:

  • Description of TNT's parallelization implementation.
  • Porting TNT's PVM-based parallelization to MPI.
  • Reanalysis of seven large-scale phylogenetic datasets using the new MPI routines.

Main Results:

  • Successful porting of TNT's parallelization to MPI.
  • Demonstrated efficiency on large phylogenomic datasets (up to 2,509,064 characters) and large taxon sets (up to 13,921 taxa).
  • Availability of MPI-enabled TNT versions.

Conclusions:

  • The MPI port enhances TNT's usability for high-performance computing.
  • This advancement enables faster and more scalable phylogenetic inference.
  • Researchers can now leverage modern parallel computing standards for complex phylogenetic analyses.