HyPhy: hypothesis testing using phylogenies. HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. It features a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface). HyPhy has over 10000 registered users and has been cited in over 1800 peer-reviewed publications (Google Scholar).

References in zbMATH (referenced in 5 articles )

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  1. Ostash, Bohdan; Anisimova, Maria: Visualizing codon usage within and across genomes: concepts and tools (2020)
  2. Stephanie J. Spielman: phyphy: Python package for facilitating the execution and parsing of HyPhy standard analyses (2018) not zbMATH
  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  4. Lemey, Philippe; Lott, Martin; Martin, Darren P.; Moulton, Vincent: Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning (2009) ioport
  5. Arenas, Miguel; Posada, David: Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography (2007) ioport