Resources#

• Check out our YouTube page for video versions of our tutorials: HyPhy YouTube

• Tutorials for using standard methods in HyPhy to infer selection ware available here. Detailed descriptions of these methods are available here.

• Current HyPhy selection analyses output JSON-formatted files, whose contents are documented here.

• Book chapters and Powerpoints detailing HyPhy usage:

  • Quantifying Natural Selection in Coding Sequences (2016)
  • Getting Started with HyPhy
  • HyPhy Book: Estimating selection pressures on alignments of coding sequences (2007)
  • Introduction: Compartmentalization Detection
  • A comprehensive selection analysis tutorial (2017)

• Getting help

  • See the current Github Issues page for posting questions or searching queries from other users.
  • The retired (as of 2014) user forum is also available for viewing here.
  • You can also tweet us at @hyphy_software with quick questions.

• Preprints for upcoming methods:

  • Extra base hits: widespread empirical support for instantaneous multiple-nucleotide changes (2020)