Title Page

Mega2 Documentation Contents

• I - Overview of Mega2
  1. Downloading and installation [New]
  2. Changes from previous release [Updated]
  3. Updated bug list [Updated]
  4. Plotting lod scores (some options)
  5. Running Mega2 in batch mode [Updated]
  6. Utility Scripts
  7. Mega2 logs and related files [Updated]
• II - Input files and their formats
  1. Locus datafile
     - Using a names file instead.
  2. Pedigree datafile
     - Using unique person IDs
     - Defining missing values
     - Handling of loops
          -- Loop breaking
          -- Loop reconnection
  3. Map datafile
     - Specifying sex-specific maps
  4. Omit datafile [Optional]
     
• III - The input menu

  Item 1: Chromosome number

  Item 2: Input file extension (optional)

  Item 3: Locus datafile

  Item 4: Pedigree datafile

  Item 5: Map datafile

  Item 6: Omit datafile(optional)

  Item 7: Directory for writing output

  Item 8: Genotyping error simulation option

  Item 9: Untyped pedigree exclusion option

• IV - The Analysis menu

  Option 1: SimWalk2 format	[Details]
  Option 2: Old MENDEL 3 format	[Details]
  Option 3: ASPEX format	[Details]
  Option 4: GeneHunter-Plus format	[Details]
  Option 5: GeneHunter format	[Details]
  Option 6: APM format	[Details]
  Option 7: APM MULT format	[Details]
  Option 8: Create nuclear families	[Details]
  Option 9: SLINK format	[Details]
  Option 10: SPLINK format	[Details]
  Option 11: Homogeneity analyses	[Details]
  Option 12: SIMULATE format	[Details]
  Option 13: Create summary files	[Details]
  Option 14: SAGE format	[Details]
  Option 15: TDTMax analyses	[Details]
  Option 16: SOLAR format	[Details]
  Option 17: Vitesse format	[Details]
  Option 18: Linkage format	[Details]
  Option 19: Test loci for HWE	[Details]
  Option 20: Allegro format	[Details]
  Option 21: MLBQTL format	[Details]
  Option 22: S.A.G.E. 4.0b format	[Details]
  Option 23: Pre-makeped format	[Details]
  Option 24: Merlin/SimWalk2-NPL	[Details]
  Option 25: PREST format	[Details]
  Option 26: PAP format	[Details]
  Option 27: Merlin format	[Details]
  Option 28: LOKI format	[Details]
  Option 29: MENDEL 5 format [New]	[Details]

• V - The locus reordering menu

  Option 1: Select all loci in map order on chromosome: ##

  Option 2: Select by locus number.

  Option 3: Select one chromosome and select loci on it.

  Option 4: Select one or more chromosomes and select loci on them.

  HINTS

• VI - The trait selection menu[Updated]

  Option 1:Select trait loci

  Option 2:For multiple trait loci, analyse traits one at a time, or combine.

  New covariate selection item.

  More details on trait selection.

• VII - Troubleshooting
  1. Dos-format file related problems
  2. Non dos related problems
  3. Genotype reset menu
• More detailed information on specific options
  • Details on: 1) SimWalk2 format
  • Details on: 2) Old MENDEL 3 format
  • Details on: 3) ASPEX format
  • Details on: 4) GeneHunter-Plus format
  • Details on: 5) GeneHunter format
  • Details on: 6) APM format
  • Details on: 7) APM MULT format
  • Details on: 8) Create nuclear families
  • Details on: 9) SLINK format
  • Details on: 10) SPLINK format
  • Details on: 11) Homogeneity analyses
  • Details on: 12) SIMULATE format files
  • Details on: 13) Create summary files
  • Details on: 14) SAGE format
  • Details on: 15) TDTMax analyses
  • Details on: 16) SOLAR format
  • Details on: 17) Vitesse format
  • Details on: 18) Linkage format
  • Details on: 19) Test loci for HWE
  • Details on: 20) Allegro format
  • Details on: 21) MLBQTL format
  • Details on: 22) S.A.G.E. 4.0 format
  • Details on: 23) Pre-makeped format
  • Details on: 24) Merlin/SimWalk2-NPL
  • Details on: 25) PREST format
  • Details on: 26) PAP format
  • Details on: 27) Merlin format
  • Details on: 28) LOKI format
  • Details on: 29) MENDEL 5 format
• Reference list for the supported programs
  
• GRANT ACKNOWLEDGEMENTS:
  
• References: