phyphy documentation

phyphy is a Python package for facilitating HyPhy (http://hyphy.org/) analysis execution and parsing. phyphy is compatible with HyPhy version >= 2.3.7.

Overview

phyphy can automate the execution and output parsing for the following standard analyses:

phyphy usage relies on three primary modules:

  • Hyphy
    • This module can be optionally used to specify that a non-canonical (i.e. not installed to /usr/local/) installation or a local build of HyPhy. This module can additionally be used to specify that HyPhy be run quietly and/or without outputting its standard log files, messages.log and errors.log.
  • Analysis
    • This module contains the analysis methods to execute, named according to the analysis. For example, the FEL class within the Analysis module would be used to execute an FEL analysis.
  • Extractor
    • This module contains functionality to parse a given analysis output. Extractor makes it simple to extract information from a given analysis JSON output, including:
      • Fitted model parameters
      • Fitted phylogenies
      • Newick-extended format phylogenies with branch features for downstream visualization
      • CSV files, for methods FEL, MEME, SLAC, FUBAR, LEISR, aBSREL

Download/Installation

phyphy is freely available under a FreeBSD license. The easiest way to install phyphy is using pip (or pip3, for use with Python3 instead of Python2.7).

sudo pip install phyphy

Alternatively, the most recent release of Phyphy is available for download from https://github.com/sjspielman/phyphy/releases. Once Pyvolve has been downloaded, navigate to the directory in the terminal. To install for all users, enter this command:

sudo python setup.py install

Alternatively, to install locally for a specific user (or if you do not have root privileges), enter this command:

python setup.py install --user

Optional tests (Python2.7 compatible only!) may be run with the command (which may or may not require sudo, depending on your install choice),

python setup.py test

Further note that phyphy has the following dependencies which must be installed (pip should take care of these for you):

  1. BioPython
  2. ete3

Issues and Questions

Please file all bugs, issues, feature requests, and/or questions in the Issues section of the phyphy github repository: https://github.com/sjspielman/phyphy/issues. Note that you will need a github account to file.

Citation

Forthcoming

Indices and tables