RealPhy - the "Reference alignment based phylogeny builder", is a java-based pipeline that leverages several third party applications that is used to infer phylogenetic trees. Applications used by the RealPhy pipeline include bowtie2, raxml, tree-puzzle, Phylip, R, and PhyML.
RealPhy may be used in the form of an on-line tool, or as a standalone application. To access and use the command-line version of RealPhy on the HPCC:
The RealPhy binaries contain special path variables that must be set inside a file named "config.txt" in order to use the pipeline. That is, simply loading the standard module files or setting those variables inside the module file are inadequate, and the authors have written RealPhy to look for and obtain those settings from config.txt.
To start RealPhy, first ensure that a copy of "config.txt" is placed inside the output directory folder (which is specified as a command line argument). To aid in using Realphy, a valid config.txt file is provided on the HPCC here:
Simply copy this file to your output directory before running.
Please consult the RealPhy Manual for detailed information on using RealPhy.