The input menu

When first started up, Mega2 will present an input menu for entering input file names and the chromosome number:

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                         Mega2 input menu:
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0) Done with this menu - please proceed
 1) Chromosome number:           1
 2) Input file extension:       01
 3) Locus datafile:              _
 4) Pedigree datafile:           _
 5) Map datafile:                _
 6) Omit datafile (optional):    _
 7) Directory for writing output:     [ Current directory ]
 8) Simulate genotyping errors:       [no ]
 9) Include all pedigrees whether typed or not

1) Chromosome number:

When the chromosome number is specified, in order to help the user, Mega2 will automatically retrieve the datain.##, pedin.##, map.##, and omit.## files (if they exist in the current directory), where ## represents the user-specified chromosome number. For example, if the user enters “1” via this menu option, then Mega2 looks for the files “datain.01”, “pedin.01”, “map.01”, and “omit.01”. 

2) Input file extension (optional):

When the input file extension (##) is specified, Mega2 will search through the current directory and retrieve the files named datain.##, pedin.##, map.##, and omit.## if they exist. Specifying the input file extension will replace the file names which were automatically filled in (if any) by specifying the chromosome number.

3) Locus datafile:

This specifies the locus file name.

4) Pedigree datafile:

This specifies the pedigree file name.

5) Map datafile:

This specifies the name of map file. The locus datafile, pedigree datafile and the map datafile are now mandatory for all Mega2 options. If the input pedigree and locus data do not contain mapped loci, then a dummy map file should be created with a single marker, which need not be included in the pedigree and locus files. See the locus reordering section for more details.

6) Omit datafile (optional):

7) Directory for writing output:

This specifies the name of the directory where Mega2 creates the output files. By default, this is set to the directory from which Mega2 is invoked. The output directory can be specified either as an absolute path (e.g. /home/nandita/mega2_results/example) or a relative path. Mega2 checks to see if the specified directory exists, if not, the user is asked if this directory should be created before proceeding.

8) Set up for simulating genotyping errors:

This option can be toggled between yes and no by simply selecting option 8 of the input menu. The default value is no. Setting this option to "yes" will cause Mega2 to execute a genotyping error simulation step after selection and reordering of marker loci. In this step, genotypes of individuals are changed at user-selected marker loci, according to a user-specified error-probability model. See Mistyping Simulation for more details.

9) Untyped pedigree exclusion option:

This specifies the minimum number of typed members a pedigree should have in order to be included in the output. Selecting this option displays the following submenu:

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Untyped pedigree exclusion options:
0) Done with this menu - please proceed.
 1) Omit any completely untyped pedigrees
*2) Include all pedigrees whether typed or not
 3) Exclude pedigrees not fully typed at one or more markers
 4) Exclude any pedigree with 1 or less marker-typed people