title: ExaML version 3: a tool for phylogenomic analyses on supercomputers.
abstract: BACKGROUND
  Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers.
  
  
  RESULTS
  We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms.
authors.affiliation: Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany and.
authors.forename: Alexey M
authors.initials: AM
authors.lastname: Kozlov
authors.affiliation: Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany and.
authors.forename: Andre J
authors.initials: AJ
authors.lastname: Aberer
authors.affiliation: Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany and Department of informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003201:Computers; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
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