An FPGA hardware acceleration of the indirect calculation of tree lengths method for phylogenetic tree reconstruction

Abstract

In this work, we present an FPGA hardware implementation for a phylogenetic tree reconstruction with maximum parsimony algorithm. We base our approach on a particular stochastic local search algorithm that uses the Indirect Calculation of Tree Lengths method and the Progressive Neighborhood. In our implementation, we define a tree structure, and accelerate the search by parallel and pipeline processing. We show results for six real-world biological datasets. We compare execution times against our previous hardware approach, and TNT, the fastest available parsimony program. Acceleration rates between 34 to 45 per rearrangement, and 2 to 6, for the whole search, are obtained against our previous approach. Acceleration rates between 2 to 4 per rearrangement, and 18 to 112, for the whole search, are obtained against TNT. We estimate that these acceleration rates could increase for even larger datasets.