Converted document

1: Introduction

1.1: Overview of Mega2

1.2: Graphical overview of Mega2 (from 2013)

1.3: Overview of Mega2R

1.4: Overview of the parallel capabilities of Mega2

1.5: Graphical overview of Mega2R (from 2017)

1.6: Supported formats

1.6.1: Input formats

1.6.2: Mega2 output formats

1.6.3: Mega2R output formats

2: Download Mega2

3: Recent improvements and changes

3.1: Enhancements in Mega2 version 6.0.0

3.2: Enhancements in Mega2 version 5.0.1

3.3: Enhancements in Mega2 version 5.0.0

3.4: Enhancements in Mega2 version 4.9.2

4: Quick start - get Mega2 running in minutes

4.1: The fast, easy way to set up your files for Mega2

4.2: Tips on more complex data

4.3: Word of caution regarding input file names

5: Citing Mega2

6: Support, bug reports, and feedback

6.1: Mega2 feedback

6.2: Mega2 Google Group

6.3: Bug reports

7: Contact information

8: Installation

8.1: Download Instructions

8.1.1: Mega2 Bitbucket repository

8.2: Prerequisites for Mega2

8.2.2: R Libraries

8.3: Installing Mega2 from a Binary Package

8.3.1: Contents of a binary package

8.3.2: Mega2 Binaries

8.3.3: Installing Mega2

8.4: Compiling and Installing Mega2 from Source

8.5: Running Mega2 on Your Data

8.6: Mega2 Documentation

8.7: License Agreement

8.8: Feedback and Bug Reports

8.9: Macintosh-specific installation issues

8.9.1: Introduction to Command line programs for Mac users

8.9.2: Xcode compilation environment

8.10: Unix-specific installation issues

8.11: Windows Cygwin installation

8.11.1: Cygwin POSIX windows environment

8.11.2: R installation:

8.11.3: Mega2 Download instructions for Windows

8.12: Windows Mingw installation

8.12.1: Mingw POSIX windows environment

8.13: Windows Msys2/Mingw64 installation

8.13.1: Msys2/Mingw64 POSIX windows environment

8.14: Native Windows installation

8.14.1: Native Windows environment

8.15: Windows Linux Subsystem installation

8.15.1: Installation of Windows for Linux

9: Supported Input file formats

9.1: Mega2 input file formats

9.1.1: Mega2 Names file

9.1.2: Mega2 Pedigree file

9.1.3: Mega2 Map file

9.1.4: Omit file

9.1.5: Frequency file

9.1.6: Penetrance file

9.2: PLINK input file formats

9.2.1: PLINK PED input format

9.2.2: PLINK binary PED input format

9.3: LINKAGE input file formats

9.3.1: LINKAGE locus file

9.3.2: LINKAGE pedigree file

9.3.3: Handling of loops inside pedigrees

9.3.4: Simple Mega2 Map file

9.3.5: Specifying sex-specific maps

9.3.6: Omit file [Optional]

9.3.7: Header-less Names file

9.4: Variant Call Format (VCF, BCF, compressed VCF) input file formats

9.4.1: Variant Call File

9.4.2: PLINK family File

9.4.3: Augmented PLINK Phenotype File

9.4.4: Map File (Optional)

9.4.5: Omit File (Optional)

9.4.6: Frequency File (Optional)

9.4.7: Penetrance File (Optional)

9.5: IMPUTE2/Oxford (GEN) and binary IMPUTE2 (BGEN) input file formats

9.5.1: IMPUTE2 standard file extensions

9.5.2: IMPUTE2 GEN File

9.5.3: IMPUTE2 Sample File

9.5.4: IMPUTE2 Info File (Optional)

9.5.5: Map File (Optional)

9.5.6: Omit File (Optional)

9.5.7: Frequency File (Optional)

9.5.8: Penetrance File (Optional)

10: Genetic Map Interpolator (GMI)

11: The Mega2R R package

12: Converting to Mega2’s format

12.1: Pedigree file conversion

12.2: Locus file conversion

12.3: Map file conversion

13: The database mode menu

14: The file input menu

14.1: Mega2 file input menu

14.2: Input formats: Mega2 and Linkage

14.3: Common PLINK menu items

14.4: Input format: PLINK binary PED

14.5: Input format: PLINK ped

14.6: Common Variant Call Format menu items

14.7: Input format: Variant Call Format files

14.8: Input format: IMPUTE2/Oxford GEN and binary IMPUTE2 BGEN Format files

14.9: Input Format: BCF v2.2 or higher utilizing BCFtools

14.9.1: BCF v2.2 or higher menu

Subsubsection: Menu item: PLINK parameters

Subsubsection: Menu item: Input file stem

Subsubsection: Menu item: BCFtools parameters

Subsubsection: Menu item: Data file or Manifest file

Subsubsection: Menu item: Pedigree File

14.10: Input Format: VCF in Compressed Format utilizing BCFtools

14.11: Input Format: VCF Format utilizing BCFtools

14.12: File input menu items: Omit, frequency and penetrance data files (optional):

14.13: File input menu item: Output Directory:

14.14: File input menu item: SQLite3 Database file:

14.15: External Reference Allele Panel

14.16: File input menu item: Simulating genotyping errors:

Subsection: Genotyping error simulation

Subsection: Parameter selection menu

Subsection: Error simulation output files

14.17: File input menu item: Untyped pedigree exclusion option:

14.18: File input menu item: Upper limit for squared deviation between input and observed allele frequencies

14.19: File input menu item: Show pedigree typing statistics

14.20: File input menu item: Unknown allele and affection definition

14.21: File input menu item: Maximum number of alleles per marker

14.22: Errors in input data

14.22.1: Problems with locus data

14.22.2: Problems with pedigree data.

14.22.3: Genotype reset menu

15: The database input menu

16: The analysis menu

17: The missing value menu

18: The allele frequency menu

18.1: The recoding process

18.2: The recode log file

18.3: Penetrances for affection status loci

19: The locus reordering menu

19.1: Locus reordering option 1) Select all loci in map order on chromosome.

19.2: Locus reordering option 2) Select by locus number.

19.3: Locus reordering option 3) Select marker loci on multiple chromosomes.

20: Map Selection Menus

20.1: The Genetic Map Selection Menu

20.2: The Physical Map Selection Menu

21: The trait selection menu

21.1: Select multiple trait loci to loop across.

21.2: Use trait loci in specified order.

21.3: List of selected trait loci

21.4: Selection of covariates

21.5: More details on trait selection.

21.6: Affection status labels

22: Creating plots using Mega2

22.1: Statistics selection menu

22.2: R-plot parameters menu

22.3: General usage of nplplot and nplplot.multi

23: Custom tracks for the UCSC Browser

24: Additional Mega2 Output Files

24.1: Summary file directory

24.2: MEGA2.LOG (and MEGA2.DB.LOG)

24.3: MEGA2.ERR (and MEGA2.DB.ERR)

24.4: MEGA2.BATCH

24.5: MEGA2.KEYS

24.6: MEGA2.SIM

24.7: MEGA2.RECODE

24.8: MEGA2run.html and related files

25: Mega2 command-line arguments

25.1: Database options

25.2: Species options

25.3: Input format options

25.4: Missing Value options

25.5: General options

25.6: Obsolete options

25.7: Other arguments

26: Running Mega2 in Batch mode

26.2: Using the --nosave option

26.3: Batch file format

26.4: Major classes of batch file options

26.5: Details on batch file items

27: Hints and troubleshooting

27.1: Hints on loci reordering

27.2: Problems commonly encountered with input files:

27.3: Pedigree file reading problem

27.4: Mega2 hangs while reading in input files

27.5: DOS format file related errors

27.5.1: Error messages

27.6: Non-DOS related problems

28: Detailed information on analysis options

28.1: Create SimWalk2 format files

28.2: Convert to Vintage MENDEL format

28.3: Convert to ASPEX format

28.4: Convert to GeneHunter-Plus format

28.5: Convert to GeneHunter format

28.6: Convert to APM format [DISABLED]

28.7: Convert to APM MULT multiple locus format [DISABLED]

28.8: Create nuclear families

28.9: Convert to SLINK format

28.10: Convert to SPLINK format

28.11: Set up for homogeneity analyses

28.12: Convert to SIMULATE format

28.13: Create summary files

28.14: Convert to Old SAGE format

28.15: Set up for TDTMax analyses [DISABLED]

28.16: Convert to SOLAR format

28.17: Convert to Vitesse format

28.18: Convert to Linkage format

28.19: Test loci for HWE (Hardy-Weinberg Equilibrium)

28.20: Convert to Allegro format

28.21: Convert to MLBQTL format

28.22: Convert to S.A.G.E. 4.0 format

28.23: Convert to pre-makeped format

28.24: Convert to Merlin-SimWalk2 combined analysis format

28.25: Convert to PREST format

28.26: Convert to PAP format

28.27: Convert to Merlin format

28.28: Convert to Loki format

28.29: Convert to Mendel format

28.30: Convert to SUP format

28.31: Convert to PLINK format

28.32: Convert to Cranefoot format

28.33: Convert to Mega2 format

28.34: Convert to IQLS/Idcoefs format

28.35: Convert to FBAT format

28.36: Convert to PANGAEA MORGAN format

28.37: Convert to Beagle format

28.38: Convert to Eigenstrat format

28.39: Convert to Structure format

28.40: Convert to PSEQ (PLINK/SEQ) format

28.41: Convert to SHAPEIT format

28.42: Convert to ROADTRIPS format

28.43: Convert to MaCH/Minimac3 format

28.44: Convert to SHAPEIT/Minimac3 format

28.45: Convert to BCF/VCF format

28.46: Convert to MQLS-XM/KinInbcoef format

29: Utilities included with Mega2

29.1: Converting linkage format files to Mega2 format - l2a.py

29.2: Map making utilities

29.3: Creating a Mega2 omit file

29.4: Scripts to generate formatted output for Hardy-Weinberg test:

30: List of third-party applications used by Mega2

30.1: R statistical package and its libraries

30.1.1: R Installation

30.2.1: Python Installation

30.3.1: Perl Installation

30.4.1: Awk Installation

31: Changes made to Mega2

31.1: Incorporation of SQLite3 into Mega2

31.2: Recent releases

31.3: Changes from Version 6.0.0 to Version 6.0.0 (Released June 15, 2019)

31.4: Changes from Version 5.0.0 to Version 6.0.0 (Released December 13, 2018)

31.5: Changes from Version 4.9.2 to Version 5.0.0 (Released June 14, 2018)

31.6: Changes from Version 4.9.1 to Version 4.9.2 (Released June 14, 2017)

31.7: Changes from Version 4.9.0 to Version 4.9.1 (Released November 1, 2016)

31.8: Changes from Version 4.8.2 to Version 4.9.0 (Released June 14, 2016)

31.9: Changes from Version 4.8.1 to Version 4.8.2 (Released January 15, 2016)

31.10: Changes from Version 4.8.0 to Version 4.8.1 (Released October 22, 2015)

31.11: Changes from Version 4.7.1 to Version 4.8.0 (Released June 13, 2015)

31.12: Changes from Version 4.6.2 to Version 4.7.1 (Released Oct 16, 2014)

31.13: Changes from Version 4.6.2 to Version 4.7.0 (Released May 15, 2014)

31.14: Changes from Version 4.6.1 to Version 4.6.2 (Released Feb 28, 2014)

31.15: Changes from Version 4.6.0 to Version 4.6.1 (Released Oct 21st, 2013)

31.16: Changes from Version 4.5.9 to Version 4.6.0 (Released Sept 6th, 2013)

31.17: Changes from Version 4.5.8 to Version 4.5.9 (Released July 5th, 2013)

31.18: Changes from Version 4.5.7 to Version 4.5.8 (Released June 6th, 2013)

31.19: Changes from Version 4.5.6 to Version 4.5.7 (Released January 11th, 2013)

31.20: Changes from Version 4.5.5 to Version 4.5.6 (Released July 6th, 2012)

31.21: Changes from Version 4.5.4 to Version 4.5.5 (Released June 15th, 2012)

31.22: Changes from Version 4.5.3 to Version 4.5.4 (Released July 26th, 2011)

31.23: Changes from Version 4.0 R5.2 Beta - Version 4.5.3 (Released June 15th, 2011)

Subsection: Changes from Ver 4.0 R5.1 - Ver 4.0 R5.2 Beta

Subsection: Changes from Ver 4.0 R5.0 - Ver 4.0 R5.1 (Released June 15th, 2010)

Subsection: Changes from Ver 4.0 R4.0 - Ver 4.0 R5.0 (Released Dec 31st, 2009)

Subsection: Changes from Ver 4.0 R3.1 - Ver 4.0 R4.0 (Released October 4th, 2009)

Subsection: Changes from Ver 4.0 R3 - Ver 4.0 R3.1 (Released July 12, 2009)

Subsection: Changes from Ver 4.0 R2 - Ver 4.0 R3 (Released Jun 15, 2009)

Subsection: Changes from Ver 4.0 R1 - Ver 4.0 R2 (Released April 15, 2009)

Subsection: Changes from Ver 4.0 - Ver 4.0 R1 (Released Jun 13, 2008)

Subsection: Changes from Ver 4.0 Beta R1 - Ver 4.0 (Released March 31, 2008)

Subsection: Changes from Ver 4.0 Beta- Ver 4.0 Beta R1 (Released August 7, 2007)

Subsection: Changes from Ver 3.0 R11- Ver 3.0 R12 and Ver 4.0 Beta (Released June 14, 2007)

Subsection: Changes from Ver 3.0 R10- Ver 3.0 R11 (Released May 17, 2007)

Subsection: Changes from Ver 3.0 R9- Ver 3.0 R10 (Released February 1, 2007)

Subsection: Very old versions

Subsection: Changes from Ver 3.0 R8- Ver 3.0 R9 (Released July 14, 2006)

Subsection: Changes from Ver 3.0 R7- Ver 3.0 R8 (Released June 19, 2006)

Subsection: Changes from Ver 3.0 R5,R6 - Ver 3.0 R7 (Released June 15, 2006)

Subsection: Changes from Ver 3.0 R4 - Ver 3.0 R5 (Released Feb 2, 2006)

Subsection: Changes from Ver 3.0 R3 - Ver 3.0 R4 (Released June 10, 2005)

Subsection: Changes from Ver 3.0 R2 - Ver 3.0 R3 (Released November 29, 2004)

Subsection: Changes from Ver 3.0 R1 - Ver 3.0 R2 (Released September 30, 2004)

Subsection: Changes from Ver 3.0 - Ver 3.0 R1 (Released August 15, 2004)

Subsection: Changes from Ver 2.5 R4 - Ver 3.0 (Released June 15, 2004)

Subsection: Changes from Ver 2.5 R3 - Ver 2.5 R4 (Released April 22, 2004)

Subsection: Changes from Ver 2.5 R2 - Ver 2.5 R3 (Released April 15, 2004)

Subsection: Changes from Ver 2.5 R1 - Ver 2.5 R2 (Released August 8, 2003)

Subsection: Changes from Ver 2.5 - Ver 2.5 R1 (Released July 5th, 2003)

Subsection: Changes from Ver 2.3 R4 - Ver 2.5 (Released June 3, 2003)

Subsection: Changes from Ver 2.3 R3 - Ver 2.3 R4 (Released Feb 7, 2003)

Subsection: Changes from Ver 2.3 R2 - Ver 2.3 R3 (Released Dec 13, 2002)

Subsection: Changes from Ver 2.3 - Ver 2.3 R2 (Released July 20 2002)

Subsection: Changes from Ver 2.2 R3 - Ver 2.3 (Released June 14 2002)

Subsection: Changes from Ver 2.2 R2 - Ver 2.2 R3 (Released January 23rd, 2002)

Subsection: Changes from version 2.2 - version 2.2 R2 (Released 28th June 2001)

Subsection: Changes from version 2.1 beta R3 - version 2.2 (Released 15 Jun 2001)

Subsection: Changes from version 2.1 beta R2 - version 2.1 beta R3 (Released 30 Mar 2001)

Subsection: Changes from version 2.1 beta - version 2.1 beta R2 (Released 16 Mar 2001)

Subsection: Changes from version 2.05 to version 2.1 beta (Released 16 Feb 2001)

32: List of fixed bugs

Subsection: Bugs in Mega2 4.0 R5.2 Beta

Subsection: Bugs in Mega2 4 R5.1

Subsection: Bugs in Mega2 4 R5.0

Subsection: Bugs in Mega2 4 R4.0

Subsection: Bugs in Mega2 4 R3.1

Subsection: Bugs in Mega2 4 R3

Subsection: Bugs in Mega2 4.0 R1

Subsection: Bugs in Mega2 4.0

Subsection: Bugs in Mega2 4.0 beta R1

Subsection: Bugs in Mega2 4.0 beta

Subsection: Bugs in Mega2 3.0 R11

Subsection: Bugs in Mega2 3.0 R10

Subsection: Bugs in Mega2 3.0 R9

Subsection: Bugs in Mega2 3.0 R8

Subsection: Bugs in Mega2 3.0 R7

Subsection: Bugs in Mega2 3.0 R5, R6

Subsection: Bugs in Mega2 3.0 R4

Subsection: Bugs in Mega2 3.0 R3

Subsection: Bugs in Mega2 3.0 R2

Subsection: Bugs in Mega2 3.0 R1

Subsection: Bugs in Mega2 3.0

Subsection: Bugs in Mega2 2.5 R4

Subsection: Bugs in Mega2 2.5 R3

Subsection: Bugs in Mega2 2.5 R2

Subsection: Bugs in Mega2 2.5 R1

Subsection: Bugs in Mega2 2.5

Subsection: Bugs in Mega2 2.3 R4

Subsection: Bugs in Mega2 2.3 R3

Subsection: Bugs in Mega2 2.3 R2

Subsection: Bugs in Mega2 2.3 and Mega2 2.3 R1

Subsection: Bugs in Mega2 2.2 R3

Subsection: Bugs in Mega2 2.2 R2

Subsection: Bugs in Mega2 2.2

Subsection: Bugs in Mega2 2.1 beta

33: License agreements

33.1: GNU General Public License Version 3 for Mega2

33.2: MIT License for VCFtools

33.3: License for ZLIB

33.4: GNU Lesser General Public License Version 3 for VCFtools and BCFtools

33.5: Boost License for BGEN

33.6: Acknowledgement of SQLite3

34: PDF documentation

35: Grant Acknowledgments