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Usage: MEGA-CC.exe -a /pathTo/analysisFile.mao -d /pathTo/dataFile.meg [-t /pathTo/treeFile.nwk][OPTIONS]

   -a --analysisOptions 
       MEGA Analysis Options File     *required*
       Specify the full path to the Mega Analysis Options (.mao) file.  
       This file tells MEGA-CC which analysis to perform as well as
       which options to use

   -c --calibration 
       Calibration file *optional*
       Specify the full path to a calibration file that you wish to use. The calibration 
       file is used to provide calibration data for tree timing methods.

   -d --data 
       Data File         *required*
       Specify the full  or relative path to the data file you wish to 
       analyze.  MEGA (.meg), and Fasta files are supported for 
       all analyses. For distance matrices the MEGA (.meg) format is required.

   -f --format *applies to sequence alignment only*
       Export format for sequence alignment
       Sequence alignments can be exported in either the native .meg
       or FASTA format.
       Format values:
         MEGA
         Fasta

   -g --groups 
       Groups file *optional*
       Specify the full path to the groups file that you wish to use. This file organizes 
       taxa into groups where each line in the file is a key value pair of the form 
             taxonName=groupName 
       Group information is used for certain analyses, for instance, specifying which taxon/taxa 
       comprise the outgroup for the timetree analysis 

   -h --help 
       Help
       Prints this help file document
   -n --noSummary: Do not write out the analysis summary file
       By default a file that gives an analysis summary is written.
       This option suppresses the export of that file. However, if
       any important messages are generated by the application, they
       will be written to this file regardless.

   -o --outfile     *optional*
       Output Path / Output Dir
       Specify the full path and base filename (e.g. /myResultsDirectory/myResultName) or
       simply the full path and directory of where to save the file
       (e.g. /myResultsDirectory) in which case, a unique filename will be chosen
       automatically for you.
   -r --recursive
       Recursive directory search *optional*
       If a directory is specified for analysis by default MEGA only searches
       the contents of that folder and not any of it's children.  To include the
       contents of all folders under the one specified, use this option.

   -s --silent: Do not write out the progress updates
       This option prevents progress updates from being written to stdout.

   -t --tree     *required for some analyses*
       Tree File
       Specify the full path to the tree file you wish to use. (Some 
       analyses requires a user provided tree, or allow you to provide 
       your own)

          If no output path is specified, results will be saved in the same directory
       as the input data file, with a unique name.