MEGA-R Wrapper

This wrapper allows for the integration of MEGA's compute core (MEGA-CC) into R workflows. It supports data input either via a data file (tree, sequence, or MEGA-specific filetype, .meg) or a data structure such as the APE package's tree structure. It handles providing the data to MEGA-CC, executing the job as specified by a .mao (MEGA Analysis Options) file, and reading output data back in to the appropriate R data structure.

Requirements

This wrapper requires MEGA-CC to be installed on the system path. Additionally, MEGA's prototyper is required to generate the .mao file for specifying analysis options. Both can be downloaded from the MEGA software page.

Installation

To load the package into R, run the following commands:

install.packages("devtools")
devtools::install_github("jaredgk/megarwrapper")

Usage

Currently, R-MEGA provides two functions: runMega and runMegaOnData, each with the following arguments:

Required

• analysis_file: Path to MEGA Analysis Options file
• data_file/data: For runMega, name of input data file. For runMegaOnData, either a DNAbin object (FASTA sequence from APE) or phylo object (newick tree from APE)

Optional

• calib_file: Path to file with calibrations for timetree/reltime analysis
• groups_file: Path to file with group definitions for taxons
• tree_file: Path to newick tree file
• out_prefix: Prefix to use for temporary output files
• temp_input_prefix: Prefix to use for filename for input data
• keep_input: If true, will delete temporary input file after analysis completes

Output

Will return a named list where names are the file extension of the output MEGA file, and the values are the data stored in those files. CSV and trees (nwk/tre) will be read in to their apporopriate data structure.