Parameters in file mainparams.

The user will need to set all of these parameters before running the program. Several of these parameters (LABEL, POPDATA, POPFLAG, PHENOTYPE, EXTRACOLS) indicate whether particular types of data are present in the input file; these are described in Section 3.

INFILE (string) Name of input data file. Max length 30 characters (or possibly less depending on operating system).

OUTFILE (string) Name for program output files (the suffixes ``_1'', ``_2'', ...,``_$m$'' (for intermediate results) and ``_f'' (final results) are added to this name). Existing files with these names will be overwritten. Max length of name 30 characters (or possibly less depending on operating system).

NUMINDS (int) Number of diploid individuals in data file.

NUMLOCI (int) Number of loci in data file.

LABEL (Boolean) Input file contains labels (names) for each individual. 1 = Yes; 0 = No.

POPDATA (Boolean) Input file contains a user-defined population-of-origin for each individual. 1 = Yes; 0 = No.

POPFLAG (Boolean) Input file contains an indicator variable which says whether to use popinfo when USEPOPINFO==1 (see below). 1 = Yes; 0 = No.

PHENOTYPE (Boolean) Input file contains a column of phenotype information. 1 = Yes; 0 = No.

EXTRACOLS (int) Number of additional columns of data after the Phenotype before the genotype data start. These are ignored by the program. 0 = no extra columns.

PHASEINFO (Boolean) The row(s) of genotype data for each individual are followed by a row of information about haplotype phase. This is for use with the linkage model only. See sections 3 and 4.2 for further details.

MISSING (int) Value given to missing genotype data. Must be an integer, and must not appear elsewhere in the data set. I use -9.

PLOIDY (int) Ploidy of the organism. Default is 2 (diploid).

ONEROWPERIND (Boolean) The data for each individual are arranged in a single row. E.g., for diploid data, this would mean that the two alleles for each locus are in consecutive order in the same row, rather than being arranged in the same column, in two consecutive rows. See section 3 for details about input formats.

GENENAMES (Boolean) The top row of the data file contains a list of $L$ names corresponding to the markers used.

MAPDISTANCES (Boolean) The next row of the data file (or the first row if GENENAMES==0) contains a list of mapdistances between neighboring loci.

MAXPOPS (int) Number of populations assumed for a particular run of the program. Pritchard et al. (2000a) call this $K$. Sometimes (depending on the nature of the data) there is a natural value of $K$ that can be used, otherwise $K$ can be estimated by checking the fit of the model at different values of $K$ (see Section 5).

BURNIN (int) Length of burnin period before the start of data collection. (See Section 4.1.)

NUMREPS (int) Number of MCMC reps after burnin. (See Section 4.1.)