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  1. Article

    Ready-to-use public infrastructure for global SARS-CoV-2 monitoring

    Wolfgang Maier, Simon Bray, Marius van den Beek, Dave Bouvier… in Nature Biotechnology (2021)

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  2. Protocol

    Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces

    Natural selection is a fundamental force sha** organismal evolution, as it both maintains function and enables adaptation and innovation. Viruses, with their typically short and largely coding genomes, exper...

    Stephanie J. Spielman, Steven Weaver, Stephen D. Shank… in Evolutionary Genomics (2019)

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  3. Article

    Open Access

    phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics

    While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use case...

    Stephen D. Shank, Steven Weaver, Sergei L. Kosakovsky Pond in BMC Bioinformatics (2018)

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    Detecting Signatures of Selection from DNA Sequences Using Datamonkey

    Natural selection is a fundamental process affecting all evolving populations. In the simplest case, positive selection increases the frequency of alleles that confer a fitness advantage relative to the rest o...

    Art F.Y. Poon, Simon D.W. Frost… in Bioinformatics for DNA Sequence Analysis (2009)

  5. No Access

    Chapter

    HyPhy: Hypothesis Testing Using Phylogenies

    Sergei L. Kosakovsky Pond, Spencer V. Muse in Statistical Methods in Molecular Evolution (2005)