Version

V. 4.5.4 installed in HIPPU

v. 4.5.4 installed in MURSKA

v. 4.5.4 installed in VUORI

Description

Mega2 is a utility program that can be used to convert data files from one format to another. Typically the program can be used to convert Linkage-format files to file-formats used by other programs such as SimWalk2.

For many of the program options, Mega2 sets up a C-shell script that then can automatically run the appropriate analyses.

Mega2 is currently structured so that the user proceeds through a series of menus, making choices in each one (or accepting the default values), until the desired output files are created. After the desired output files are created, Mega2 exits.

Tip: Mega2 can be used to test Hardy-Weinberg equilibrium.

Usage

To initialize the program on HIPPU and MURSKA, type:

module load mega2

Start the program by typing

mega2

Mega2 is quite simple to use because of its menu-driven interface. An example of the menu is given below.

0) Done with this menu - please proceed
1) Chromosome number: 1
2) Input file extension: 01
3) Locus datafile: datain.01
4) Pedigree datafile: pedin.01
5) Map datafile: map.01
6) Omit datafile (optional): _
Select from option 0-6 >

Mega2 typically needs three input files (see the example files):

• the locus file modified to contain locus name information

• the pedigree file

• the map file

So basically you need to modify the locus file and create a new file containing the marker map. The name of the markers must be the same in the locus and the map files.

As an example starting from the Linkage-format files (with a modified locus file and with an additional map file) Mega2 creates following SimWalk2 files if that option was selected:

Created the following SimWalk2 files
Pedigree file: PEDIGREE.01
Locus file: LOCUS.01
Penetrance file: PEN.01
Batch File: BATCH2.01
C-Shell script file: loc.01.sh

Now you can run the SimWalk2 just by typing 'loc.01.sh'.

Documentation

A complete documentation is available here.

References

If you use Mega2 as part of a published work, please remember to reference Mega2. You may reference it by citing the following:

Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (2005)

Mega2: data-handling for facilitating genetic linkage and association analyses.
Bioinformatics. 2005 May 15;21(10):2556-7.
PMID: 15746282

as well as citing the web site and the version that you used. The web site citation for version 4.2 should be:

Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (2009) Mega2 (Version 4.2). http://watson.hgen.pitt.edu

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