1. Convert to SimWalk2 format
  2. Convert to MENDEL format
  3. Convert to ASPEX format
  4. Convert to GeneHunter-Plus format
  5. Convert to GeneHunter format
  6. Convert to APM format
  7. Convert to APM MULT multiple locus format
  8. Create nuclear families
  9. Convert to SLINK format
  10. Convert to SPLINK format
  11. Set up for homogeneity analyses
  12. Convert to SIMULATE format
  13. Create summary files
  14. Convert to SAGE format
  15. Set up for TDTMax analyses
  16. Convert to SOLAR format
  17. Convert to Vitesse format
  18. Convert to Linkage format
  19. Test loci for Hardy-Weinberg Equilibrium
  20. Convert to Allegro format
  21. Convert to MLBQTL format
  22. Convert to SAGE4.0 format
  23. Pre-makeped format
  24. Merlin/SimWalk2-NPL format**
  25. PREST format
  26. PAP format
  27. Merlin format
  28. LOKI format
  29. Mendel5 format [New]

** Note that the Merlin/SimWalk2 interface option will only work with Merlin version 0.10.2 (or higher) and SimWalk2 version 2.89 (or higher), the latest releases of these two software.

IV - The Analysis menu

After all the input files and the chromosome number have been specified, then one proceeds to the Analysis menu, which presents a variety of different conversion options:

==========================================================
                 ANALYSIS MENU
==========================================================
 1 SimWalk2 format                 16 SOLAR format
 2 MENDEL format                   17 Vitesse format
 3 ASPEX format                    18 Linkage format
 4 GeneHunter-Plus format          19 Test loci for HWE
 5 GeneHunter format               20 Allegro format
 6 APM format                      21 MLBQTL format
 7 APM MULT format                 22 SAGE 4.0 format
 8 Create nuclear families         23 Pre-makeped format
 9 SLINK format                    24 Merlin/SimWalk2-NPL format
10 SPLINK format                   25 PREST format
11 Homogeneity analyses            26 PAP format
12 SIMULATE format                 27 Merlin format
13 Create summary files            28 Loki format
14 SAGE format                     29 Mendel 5 format
15 TDTMax analyses

Overview:
Note that we can not provide in depth documentation for each of the programs for which Mega2 can create files; in fact, we assume that the user will read the documentation of the appropriate program. Also, since many of these external programs are written by others, it is possible (and perhaps likely) that Mega2 will be out of synch with a newly updated version of one of these programs. If you notice this, please notify us as soon as possible.
In brief, the various options in the Analysis menu are listed below. Note that in most cases, in addition to generating appropriately re-formatted files, Mega2 also generates a C-shell script that will automatically run the desired program. However, these C-shell scripts will only function correctly if the needed programs (with the appropriate names) are in your path and installed properly on your workstation.

1. Create SimWalk2 format files

This option creates the files needed for haplotyping, parametric analysis, non-parametric analysis, or IBD estimation via the SIMWALK2 program.
Name: SIMWALK2 2.82
Web: http://watson.hgen.pitt.edu/register
Primary reference(s): (Sobel and Lange 1996)

2. Convert to MENDEL 3 format

This option creates output files in the old MENDEL 3 format.
NOTE: This option will also place the chromosome and map position information into the locus data file, as required by the RELPAIR program by Michael Boehnke and William L. Duren (Boehnke and Cox 1997).
Name: MENDEL
Web: http://www.biomath.medsch.ucla.edu/faculty/klange/software.html
Primary reference(s): (Lange et al. 1988)

3. Convert to ASPEX format

This option creates files in the appropriate format for analysis via the many modules (sib_ibd, sib_tdt, sib_phase, sib_map) of the ASPEX program. There is an option to convert larger pedigrees to their component nuclear families if needed.
Name: ASPEX
Web: http://aspex.sourceforge.net/
Primary reference(s): (Hinds and Risch 1996)

4. Convert to GeneHunter-Plus format

This option creates the files needed for analysis via the GeneHunter-Plus program.
Name: GeneHunter-Plus
Web: http://galton.uchicago.edu/genehunterplus/
Primary reference(s): (Kong and Cox 1997)

5. Convert to GeneHunter format

This option creates the files needed for analysis via the GeneHunter program.
Name: GeneHunter
Web: http://www.fhcrc.org/labs/kruglyak/Downloads/index.html
Primary reference(s): (Kruglyak et al. 1996)

6. Convert to APM format

This option creates the files needed for analysis via the Affected Pedigree Member method (single marker analyses).
Name: APM and APM Mult
Web: http://watson.hgen.pitt.edu/register
Primary reference(s): (Weeks and Lange 1988)

7. Convert to APM MULT multiple locus format

This option creates the files needed for analysis via the multilocus version of the Affected Pedigree member method.

8. Create nuclear families

This option breaks down larger pedigrees into their component nuclear families (parents plus children), and output the resulting locus and pedigree files in LINKAGE format.

9. Convert to SLINK format

This option creates the files needed for input into the simulation program SLINK.
Name: SLINK, FASTSLINK (Use FASTSLINK instead of SLINK)
Web: http://watson.hgen.pitt.edu/register
Primary reference(s): (Ott 1989; Weeks et al. 1990)

10. Convert to SPLINK format

This option creates the files needed for linkage analyses using affected sib-pairs as implemented in the SPLINK program by David Clayton.
Name: SPLINK
Web: http://www-gene.cimr.cam.ac.uk/clayton/software/
Primary reference(s): (Holmans 1993)

11. Set up for homogeneity analyses

This option creates the files needed to compute lod scores under heterogeneity, using component programs from the ANALYZE package.
Name: ANALYZE package
Web: http://www.helsinki.fi/~tsjuntun/linkage/analyze/
Primary reference(s): (Terwilliger 1996)

12. Convert to SIMULATE format

This option creates the files needed for input into the simulation program SIMULATE.
Name: SIMULATE
Web: ftp://linkage.rockefeller.edu/software/simulate
Primary reference(s): (Terwilliger et al. 1993)

13. Create summary files

This option creates summary files providing information about the segregation of the trait, counts of affected relative pairs and affected sibling pairs, marker allele frequencies (including observed and expected heterozygosity), genotyping success rate, and phenotype counts summaries. There is also an option to create counts of alleles and genotypes within categories (affection status categories or liability class categories).

The different summary options can be selected using the Summary file option sub-menu: 

 

Selection Menu: Summary file options
1) Create segregation and relative count summary files.
2) Create allele frequency summary table.
3) Count alleles and genotypes within groups.
4) Create genotyping success rate summary.
5) Create quantitative phenotype summary.
Enter selection: 1 - 5 >

14. Convert to SAGE format

This option creates the files needed for analysis via the SAGE package. This supports the old FORTRAN-like SAGE format (rather than the new more elegant format now available in beta-version).
Name: SAGE
Web: http://darwin.cwru.edu/sage/index.php
Primary reference(s):

15. Set up for TDTMax analyses

This option creates the files needed for analysis via the TDTMax program.
Name: TDTMax
Web: Current location unknown
used to be http://www.rdg.ac.uk/AcaDepts/sn/wsn1/dept/APM.html
Primary reference(s): (Morris et al. 1997)

16. Convert to SOLAR format

This option creates the files needed for analysis via the SOLAR package.
Name: SOLAR
Web: http://www.sfbr.org/solar/index.html
Primary reference(s): (Blangero and Almasy 1997; Almasy and Blangero 1998)

17. Convert to Vitesse format

This option creates files in LINKAGE format for analysis with Vitesse. Note that sets up shell-scripts that automate MLINK-like and LINKMAP-like analyses.

Name: Vitesse
Web: http://watson.hgen.pitt.edu/register
Primary reference(s): (O'Connell and Weeks 1995)

18. Convert to Linkage format

This option creates files in LINKAGE format. This is useful for reordering loci or selecting subsets of loci from large files.

Name: LINKAGE
Web: ftp://linkage.rockefeller.edu/software/linkage
Primary reference(s): (Lathrop and Lalouel 1984; Lathrop et al. 1986; Lathrop and Lalouel 1988)

19. Test loci for Hardy-Weinberg Equilibrium

This option permits one to test markers for Hardy-Weinberg equilibrium using either the "hwe" program by Guo and Thompson (1992) or the "Gen" program by Lazzeroni and Lange (1997).

Name: hwe
Web:
Primary reference(s): (Guo and Thompson 1992)

Name: Gen
Web:
Primary reference(s): (Lazzeroni and Lange 1997)


20. Convert to Allegro format

This option creates the files needed for analysis via the Allegro program. Further information is available at the URL below.
Name: Allegro
Web: Website not up, send email to: allegro@decode.is
Primary reference(s): Allegro, a new computer program for multipoint linkage analysis; (May 2000, Gudbjartsson DF, Jonasson K, Frigge ML, Kong A)

21. Convert to MLBQTL format

This option creates the files needed for the analysis of quantitative traits as well as affection status loci via the Maximum-Likelihood-Binomial extension of the GENHUNTER program. Please make sure that quantitative data are normalized, as required by the MLBQTL program.
Name: MLBQTL
Web: Unknown at present, used to be
ftp://ftp.biomath.jussieu.fr/pub/mlbgh/
Primary reference(s): (Alcais A, Abel L. 1999)

22. Convert to S.A.G.E. 4.0 format

This option creates the files needed for using the new SAGE 4.0 version. Currently, the user has to manually add sections required for running various SAGE 4.0 programs to the bottom of the parameter file. The pedinfo program can be run as is.
Name: S.A.G.E. 4.0 Beta 6a
Web: This is not free software, consult http://darwin.cwru.edu/sage/products.php
Primary reference(s):

23) Convert to pre-makeped format

This option will output pedigree and locus files where the pedigrees are in pre-makeped format. If the input pedigree file was in a post-makeped format, this option will also connect together loops in the output.

24. Setup for Merlin-SimWalk2 combined analysis

This option sets up one set of output data files which can be run through Merlin's NPL analysis option, and a second set which can be run through SimWlak's NPL option. It also sets up the requisite scripts that run these two programs in tandem, feeding in NPL results from Merlin to SimWalk2. To use this option, the latest versions of Merlin (0.10.2 or higher) and Simwalk2 (2.89 or higher) are required.
Name: Merlin
Web: "http://www.sph.umich.edu/csg/abecasis/Merlin "
http://watson.hgen.pitt.edu/register

25. Convert to PREST 3.0 format

This option sets up pedigree, chromosome, control and script files for analyzing with PREST (Pedigree RElationship Statistical Test) version 3.0.
Name: PREST 3.0
Web: "http://galton.uchicago.edu/~mcpeek/software/prest/"

26. Convert to PAP 5.0 format

This option sets up the files necessary for running PAP (Pedigree Analysis Package) including the triplets file (trip.dat), the phenotypes file (phen.dat), the control file (header.dat), and the locus file (popln.dat).
Name: PAP 5.0
Web: "http://hasstedt.genetics.utah.edu/"

 

27. Convert to Merlin format

This option sets up the files necessary for running Merlin including the pedigree, locus and map files.
Name: Merlin
Web: "http://www.sph.umich.edu/csg/abecasis/Merlin"

 

28. Convert to LOKI format

This option sets up the files necessary for running LOKI including the pedigree file, control files, and link files.
Name: Loki version 2.3
Web: "http://loki.homeunix.net/"

 

29. Convert to MENDEL 5 format

This option sets up the files necessary for running Mendel5 including the pedigree file, locus, map, penetrance and control file per chromosome.
Name: Mendel 5.0
Web: http://www.biomath.medsch.ucla.edu/faculty/klange/software.html
Primary reference(s): (Lange et al. 1988)