Exploring modern FPGA platforms for faster phylogeny reconstruction with RAxMLExploring modern FPGA platforms for faster phylogeny reconstruction with RAxML Δημοσίευση σε Συνέδριο Conference Publication 2022-01-072020enThe Phylogenetic Likelihood Function (PLF) is one of the cornerstone functions in most phylogenetic inference tools; its execution represents the majority of time required to complete an analysis. This work proposes the acceleration of this function using reconfigurable hardware accelerators, focusing on system-on-chips that integrate Field Programmable Gate Array (FPGA) resources as well as traditional High Performance Computing (HPC) systems that use FPGA-based accelerator cards. Taking into account the specific properties of each platform in order to exploit their processing capabilities, the proposed solutions provide significant performance gains. The measured acceleration of PLF function is up to 8x while the overall time to complete a phylogenetic analysis using the popular RAxML software can be reduced up to 3.2 times (with respect to a pure software implementation on a high-end server processor). Compared to other similar solutions proposed in literature, our systems perform up to 65% faster.http://creativecommons.org/licenses/by/4.0/97-1042020 IEEE 20th International Conference on Bioinformatics and BioengineeringProceedings - IEEE 20th International Conference on Bioinformatics and Bioengineering Malakonakis Pavlos Μαλακωνακης Παυλος Brokalakis Andreas Μπροκαλακης Ανδρεας Alachiotis Nikolaos Αλαχιωτης Νικολαος Sotiriadis Evripidis Σωτηριαδης Ευριπιδης Dollas Apostolos Δολλας Αποστολος Institute of Electrical and Electronics Engineers Phylogenetic inference Phylogenetic tree RAxML (Randomized Axelerated Maximum Likelihood) PLF (Phylogenetic Likelihood Function) Phylogenetic likelihood FPGA (Field Programmable Gate Array) Reconfigurable hardware Amazon AWS F1