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The Phylogenetic Likelihood Function (PLF) is an important statistical function for evaluating phylogenetic trees. To this end, the PLF is the computational kernel of all state-of-the-art likelihood-based phylogenetic inference programs. Typically, it accounts for more than 85% of total execution time in such programs. We present a substantially improved hardware architecture for computing the PLF...
Recent advances in molecular sequencing technology have given rise to novel algorithms for simultaneously aligning short sequence reads to reference sequence alignments and corresponding evolutionary reference trees. We present a complete hardware/software implementation for the acceleration of a program called PaPaRa, a newly introduced dynamic programming algorithm for this purpose. We verify the...
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