HyPhy

Description

hyphy website

This module enables the use of the HyPhy molecular evolution and statistical sequence analysis software package developed by members of the Viral Evolution Group at the School of Medicine at UCSD and collaborators. HyPhy is a feature rich and mature (in development since 1997), scriptable and fast maximum likelihood sequence analysis software platform with over 6000 registered users and over 500 citations in peer reviewed literature. HyPhy can fit statistical evolutionary models to alignment of homologous sequences using Maximum likelihood 2), estimate various parameters that have biological meaning, for example branch lengths, substitution rates, dN/dS ratios, recombination breakpoints, and test hypotheses about how sequences in the alignment have evolved. HyPhy focuses on inference about the evolutionary process. Even though it can do limited alignment and phylogenetic reconstruction, much better specialized programs exist for these purposes. Here are some of the applications that HyPhy is often used for: * Positive and negative selection detection * Recombination analysis * Detecting co-evolving residues * Genomic and multiple-gene evolutionary inference * Molecular clock and relative rate tests * Nucleotide, protein and codon model selection * As a likelihood analysis engine for other software and web services * One-off analyses: tasks that no other package does out of the box and are not worth writing a specialized program for This module provides a single--threaded version of HYPHY (HYPHYSP) built with GCC Compiler. There is a 'hyphy' alias that points to HYPHYSP. Modules system sets up the following environment variables for this module:

Environment Modules

Run module spider hyphy to find out what environment modules are available for this application.

Environment Variables

• HPC_HYPHY_DIR - installation directory, also available as HYPHY_BASE_DIRECTORY.
• HPC_HYPHY_BIN - executable directory

Categories

biology, genomics