Division of Statistical Genetics
Department of Human Genetics
University of Pittsburgh

Mega2 Announcement
"Manipulation Environment for Genetic Analyses"


You may obtain it here

Documentation for Mega2 may be found here

The Mega2 Google Group can be found here

Bugs may be reported via this form here

Official references:
Baron RV, Kollar C, Mukhopadhyay N, Weeks DE. Mega2: validated
data-reformatting for linkage and association analyses. Source Code Biol Med.
2014 Dec 5;9(1):26. doi: 10.1186/s13029-014-0026-y. eCollection 2014. PubMed
PMID: 25687422; PubMed Central PMCID: PMC4269913.
Link

Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE.
Mega2: data-handling for facilitating genetic linkage and association analyses.
Bioinformatics. 2005 May 15;21(10):2556-7. Epub 2005 Mar 3.
PMID: 15746282
Link

IMPORTANT: Use SimWalk2 version 2.89 (or higher) and Merlin's latest version (0.10.2 or higher) for the Merlin/SimWalk2-NPL interface option.

Mega2 data reformating capabilities

LINKAGEMega2 PLINKVCF or BCF IMPUTE2
to ASPEX format to ASPEX format to ASPEX format to ASPEX format to ASPEX format
to Allegro format to Allegro format to Allegro format to Allegro format to Allegro format
to Beagle format to Beagle format to Beagle format to Beagle format to Beagle format
to CRANEFOOT format to CRANEFOOT format to CRANEFOOT format to CRANEFOOT format to CRANEFOOT format
to Eigenstrat format to Eigenstrat format to Eigenstrat format to Eigenstrat format to Eigenstrat format
to FBAT format to FBAT format to FBAT format to FBAT format to FBAT format
to GeneHunter format to GeneHunter format to GeneHunter format to GeneHunter format to GeneHunter format
to GeneHunter-Plus format to GeneHunter-Plus format to GeneHunter-Plus format to GeneHunter-Plus format to GeneHunter-Plus format
to IQLS/Idcoefs format to IQLS/Idcoefs format to IQLS/Idcoefs format to IQLS/Idcoefs format to IQLS/Idcoefs format
to Linkage format to Linkage format to Linkage format to Linkage format to Linkage format
to Loki format to Loki format to Loki format to Loki format to Loki format
to MLBQTL format to MLBQTL format to MLBQTL format to MLBQTL format to MLBQTL format
to MaCH/minimac3 format to MaCH/minimac3 format to MaCH/minimac3 format to MaCH/minimac3 format to MaCH/minimac3 format
to Mega2 annotated format to Mega2 annotated format to Mega2 annotated format to Mega2 annotated format to Mega2 annotated format
to Mendel format to Mendel format to Mendel format to Mendel format to Mendel format
to Merlin format to Merlin format to Merlin format to Merlin format to Merlin format
to Merlin/SimWalk2-NPL format to Merlin/SimWalk2-NPL format to Merlin/SimWalk2-NPL format to Merlin/SimWalk2-NPL format to Merlin/SimWalk2-NPL format
to PANGAEA MORGAN format to PANGAEA MORGAN format to PANGAEA MORGAN format to PANGAEA MORGAN format to PANGAEA MORGAN format
to PAP format to PAP format to PAP format to PAP format to PAP format
to PLINK format to PLINK format to PLINK format to PLINK format to PLINK format
to PREST format to PREST format to PREST format to PREST format to PREST format
to PSEQ format to PSEQ format to PSEQ format to PSEQ format to PSEQ format
to Pre-makeped LINKAGE format to Pre-makeped LINKAGE format to Pre-makeped LINKAGE format to Pre-makeped LINKAGE format to Pre-makeped LINKAGE format
to ROADTRIPS format to ROADTRIPS format to ROADTRIPS format to ROADTRIPS format to ROADTRIPS format
to SAGE format to SAGE format to SAGE format to SAGE format to SAGE format
to SHAPEIT format to SHAPEIT format to SHAPEIT format to SHAPEIT format to SHAPEIT format
to SIMULATE format to SIMULATE format to SIMULATE format to SIMULATE format to SIMULATE format
to SLINK format to SLINK format to SLINK format to SLINK format to SLINK format
to SOLAR format to SOLAR format to SOLAR format to SOLAR format to SOLAR format
to SPLINK format to SPLINK format to SPLINK format to SPLINK format to SPLINK format
to SUP format to SUP format to SUP format to SUP format to SUP format
to SimWalk2 format to SimWalk2 format to SimWalk2 format to SimWalk2 format to SimWalk2 format
to Structure format to Structure format to Structure format to Structure format to Structure format
to VCF format to VCF format to VCF format to VCF format to VCF format
to Vintage Mendel format to Vintage Mendel format to Vintage Mendel format to Vintage Mendel format to Vintage Mendel format
to Vitesse format to Vitesse format to Vitesse format to Vitesse format to Vitesse format

Release history:

13 Dec 2018: Updated to Version 5.0.1
14 Jun 2018: Updated to Version 5.0.0
13 Jun 2017: Updated to Version 4.9.2
 1 Nov 2016: Updated to Version 4.9.1
13 Jun 2016: Updated to Version 4.9.0
15 Jan 2015: Updated to Version 4.8.2
22 Oct 2015: Updated to Version 4.8.1
13 Jun 2015: Updated to Version 4.8.0
17 Oct 2014: Updated to Version 4.7.1
20 May 2014: Updated to Version 4.7.0
 6 Mar 2014: Updated to Version 4.6.2
21 Oct 2013: Updated to Version 4.6.1
 9 Sep 2013: Updated to Version 4.6.0
 5 Jul 2013: Updated to Version 4.5.9
 6 Jun 2013: Updated to Version 4.5.8
11 Jan 2013: Updated to Version 4.5.7
30 Jul 2012: Updated to Version 4.5.6
15 Jun 2012: Updated to Version 4.5.5
26 Jul 2011: Updated to Version 4.5.4
15 Jun 2011: Updated to Version 4.5.3
22 Jul 2010: Updated to Version 4.5.2 beta
15 Jun 2010: Updated to Version 4.5.1
 1 Jan 2010: Updated to Version 4.5.0
 4 Oct 2009: Updated to Version 4.4.0
11 Jul 2009: Updated to Version 4.3.1
15 Jun 2009: Updated to Version 4.3
15 Apr 2009: Updated to Version 4.2
13 Jun 2008: Updated to Version 4.0 R1
31 Mar 2008: Released Version 4.0 (non-beta).
15 Oct 2007: Updated to Version 4.0 beta R1 (Version 3.0 R12 retired).
14 Jun 2007: Released Version 4.0 beta
14 Jun 2007: Updated to Version 3.0 R12
 1 Feb 2007: Updated to Version 3.0 R10
14 Jul 2006: Updated to Version 3.0 R9
19 Jun 2006: Updated to Version 3.0 R8
15 Jun 2006: Updated to Version 3.0 R7
14 Feb 2006: Updated to Version 3.0 R5
10 Jun 2005: Updated to Version 3.0 R4
29 Nov 2004: Updated to Version 3.0 R3
26 Oct 2004: Updated to Version 3.0 R2
15 Jun 2004: Updated to Version 3.0
22 Apr 2004: Updated to Version 2.5 R4
15 Apr 2004: Updated to Version 2.5 R3
 8 Aug 2003: Updated to Version 2.5 R2
 3 Jul 2003: Updated to Version 2.5 R1
 3 Jun 2003: Updated to Version 2.5
 7 Feb 2003: Updated to Version 2.3 R4
13 Dec 2002: Updated to Version 2.3 R3 
19 Jul 2002: Updated to Version 2.3 R2
14 Jun 2002: Updated to Version 2.3
23 Jan 2002: Updated to Version 2.2 R3 (Release 3)
28 Jun 2001: Updated to Version 2.2 R2 (Release 2)
20 Jun 2001: Expiration bug fixed in Version 2.2
13 Jun 2001: Updated to Version 2.2
 3 Apr 2001: Updated to Version 2.1 beta R3
16 Mar 2001: Updated to Version 2.1 beta R2
12 Feb 2001: Updated to Version 2.1 beta
16 January 2000: Mega2 has finally been released!

Contact

 Daniel E. Weeks, Ph.D.        
 Department of Human Genetics   
 University of Pittsburgh        
 Public Health 3119
 130 DeSoto Street             
 Pittsburgh, PA 15261          
 USA                          
                              
 (412) 624-5388               
 FAX: (412) 624-3020

weeks AT pitt.edu

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