HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Abstract

HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting a broad range of evolutionary models to multiple sequence alignments, and for conducting subsequent parameter estimation and hypothesis testing, primarily in the maximum likelihood statistical framework. It has become a popular choice for characterizing various aspects of the evolutionary process: natural selection, evolutionary rates, recombination, and coevolution. The 2.5 release (available from www.hyphy.org) includes a completely re-engineered computational core and analysis library that introduces new classes of evolutionary models and statistical tests, delivers substantial performance and stability enhancements, improves usability, streamlines end-to-end analysis workflows, makes it easier to develop custom analyses, and is mostly backward compatible with previous HyPhy releases.

Keywords: evolutionary analysis; hypothesis testing; natural selection; software engineering; statistical inference.

Fig. 1.

The common use of HyPhy is to fit evolutionary models and perform hypothesis testing on multiple sequence alignments with given phylogenies that are assumed to have been generated with other tools. HyPhy can be run on a desktop, either as a command-line tool for access to its complete functionality, or via a simple Electron-based graphical user interface to access the most popular analyses. Computing cluster use and pipeline integration is facilitated via flexible specification of command line arguments. Several web services, Datamonkey (Weaver et al. 2018), Galaxy (Blankenberg et al. 2010), or MEGA X (Kumar et al. 2018) incorporate HyPhy as a computational engine and provide varying sets of analysis options. Canonical analysis output is accessed in summary/report form via a Markdown document or interactively/programmatically through the detailed JSON report.