Pre-compiled packages are available as zipped archives
(archived using gnu-tar and compressed using gnu-zip) for the following platforms:

1. Each platform-specific Mega2 package contains the following files:

   • The Mega2 binary file compiled for a specific platform, named
     mega2_v3.0_[platform].tar.gz
     
     For example: the binary file for version 3.0 compiled for linux
     running on an Intel PC is named
     
     Mega2_v3.0_linux-intel.tar.gz
     

   • Perl scripts utilized by various options -
          make_gen_table.pl.src
          make_hwe_table.pl.src
          mega2log2html.pl.src
          merlin2sw2.pl.src
          Rallegro.pl.src
          Rmerlin.pl.src
          Rsimwalk2.pl.src
     
     These scripts are not directly executable, and they need to be
     installed as per directions in section E .

   • File nplplot_0.2.tar.gz (for Unix platforms).
   • File INSTALL.txt - containing these identical set of instructions.
   • File LICENSE.txt - the Mega2 license agreement.
   • File CHANGES.txt - changes made to Mega2 versions and revisions.
   • Directory example/ containing example data.
   • Directory map_making_utils/ - Utilities for creating Mega2-format map files.
     

2. Installation steps

   • Download the Mega2 distribution package that is appropriate for your machine.
   • Uncompress it using the "gunzip" Unix command. For example,

          gunzip mega2_v3.0_solaris.tar.gz 

   • Untar it using the "tar" unix command.

          tar xvf mega2_v3.0_solaris.tar

     NOTE: You may try to combine the above two steps via a single command

          tar xzvf mega2_v3.0_solaris.tar.gz

     The "z" instructs tar that it is a compressed archive. This is works for Gnu-tar.

3. At this point, you should see a new directory named mega2_v3.0_[platform]
   For example, if you downloaded mega2_v3.0_linux-intel.tar.gz, you should see a directory named mega2_v3.0_linux-intel. This directory contains the files and sub-directories listed below in alphabetical order:

   CHANGES.txt:	List of changes for this version
   example/ :	Directory of example input files
   install.sh :	Bash script for installing perl scripts and Mega2 executable
   INSTALL.txt :	File containing these instructions
   LICENSE.txt :	License agreement
   make_gen_table.pl.src :	Perl script source
   make_hwe_table.pl.src :	Perl script source
   map_making_utils/ :	Map making utilities
   mega2_v3.0_linux-intel.gz:	Mega2 binary
   mega2log2html.pl.src :	Perl script source
   merlin2sw2.pl.src :	Perl script source
   nplplot_0.2.tar.gz :	R library package
   Rallegro.pl.src :	Perl script source
   Rmerlin.pl.src :	Perl script source
   Rsimwalk2.pl.src :	Perl script source

4. The nplplot_0.2.tar.gz is a source package that installs the "nplplot" library to an existing R installation. This library is necessary if you intend to create LOD score curves for SimWalk2 and Allegro using Mega2's plotting facility.
   On a linux/Unix system, you can install the nplplot R function into R by logging in as root and then typing
   

            R CMD INSTALL nplplot_0.2.tar.gz

   
   at the Unix prompt.
   If this command is successful, when you start up R and type 'library()' at the R prompt, the 'nplplot' library should appear in the list of installed libraries.

5. Installing perl scripts: Execute the script install.sh by typing

          ./install.sh perl

   It prompts the user to enter a directory to install the perl scripts into. Enter the full path name of the desired directory
   

   e.g. /usr/local/bin/perl

   For these scripts to be accessible, the directory entered above must be in the user's path. On some platforms, you may need to type 'rehash' to refresh your search path (this is not necessary on Linux, and the rehash command is not a standard Linux command).

6. Installing Mega2 executable:Execute the script install.sh by typing

          ./install.sh mega2

   and enter the full path name as in the previous section (map be different from the one specified for the perl scripts). Mega2 can now be run on a set of data by simply typing the command "mega2" (or the appropriate executable name). It should be invoked from within the directory containing the data files.
   The two previous steps can be combined if you wish to install Mega2 as well as the perl scripts in the same path as follows:

          ./install.sh all 

7. Map-making utils: These are utility scripts contained in the "map_making_utils" directory.

8. Example dataset:
   The example/ directory should contain the following files:

            datain.05
            map.05      
            pedin.05
            pedin.pre.05
            datain.ex   
            map.ex    
            omit.ex
            pedin.ex
   	 

   These constitute two sets of datafiles, the ".05" dataset and the ".ex" dataset. The *.ex set also includes an omit file to illustrate the usage of the "omit" file. The pedin.pre.05 file is a pre-Makeped format file. It uses the datain.05 locus data file. It has to be specified by selecting option 4 of the input menu.

The documentation may be found on-line at

The distribution of this package is governed by our license agreement. Please follow the terms of this agreement. In particular, non-academic users must pay a licensing fee to the University of Pittsburgh.

If any of these instructions are not clear, please let us know via our feedback form by following the "Feedback/Bug report" link on the following page: