Porting PHYLIP phylogenetic package on the desktop GRID platform XtremWeb-CH.

Area of Science:

• Computational Biology
• Bioinformatics
• Distributed Computing

Background:

• PHYLIP is a widely-used phylogenetic package for inferring evolutionary trees.
• Sequential execution of some PHYLIP modules is computationally intensive, limiting analysis of large datasets.
• Existing grid platforms often lack a fully symmetric peer-to-peer model.

Purpose of the Study:

• To parallelize and deploy PHYLIP modules on the XtremWeb-CH desktop grid platform.
• To evaluate the performance and applicability of the parallelized PHYLIP for evolutionary analysis.
• To demonstrate the capabilities of XtremWeb-CH for high-performance computing tasks.

Main Methods:

• Porting and deployment of selected PHYLIP modules onto the XtremWeb-CH infrastructure.
• Utilizing XtremWeb-CH's symmetric peer-to-peer architecture for distributed computation.
• Execution of parallelized PHYLIP for generating phylogenetic trees.

Main Results:

• Successful parallelization and execution of PHYLIP modules on the XtremWeb-CH platform.
• Demonstrated feasibility of using desktop grids for computationally demanding phylogenetic analyses.
• Generated evolutionary trees for HIV viruses using the parallelized PHYLIP.

Conclusions:

• The parallelized PHYLIP on XtremWeb-CH offers a viable solution for accelerating phylogenetic inference.
• XtremWeb-CH provides a flexible and efficient platform for distributed scientific computing.
• This approach enhances the capacity for analyzing complex evolutionary relationships, such as those in viral evolution.