STRUCTURE documentation

Version 2.2 (April 3, 2007)
The program structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.

• written in C with Java front end
• UNIX
• Windows
• Mac OS X

• SNP
• Microsatellites
• RFLP
• AFLP
• dipoid/haploid

The entire data set is arranged as a matrix in a single file, in which the data for individuals are in rows, and the loci are in columns. For a diploid organism, data for each individual can be stored either as 2 consecutive rows, where each locus is in one column, or in one row, where each locus is in two consecutive columns.

example for the genotype data:

            loc_a  loc_b  loc_c  loc_d  loc_e
George   1   -9     145     66     0     92
George   1   -9     -9      64     0     94
Paula    1   106    142     68     1     92
Paula    1   106    148     64     0     94
Matthew  2   110    145     -9     0     92
Matthew  2   110    148     66     1     -9
Bob      2   108    142     64     1     94
Bob      2   -9     142     -9     0     94
Anja     1   112    142     -9     1     -9
Anja     1   114    142     66     1     94
Peter    1   -9     145     66     0     -9
Peter    1   110    145     -9     1     -9
Carsten  2   108    145     62     0     -9
Carsten  2   110    145     64     1     92

The basic algorithm :
Pritchard, J. K., Stephens, M., and Donnelly, P. (2000a). Inference of population structure using multilocus genotype data. Genetics, 155:945{959.

Extensions to the method:
Falush, D., Stephens, M., and Pritchard, J. K. (2003a). Inference of population structure: Exten- sions to linked loci and correlated allele frequencies. Genetics, 164:1567{1587.
and
Falush, D., Stephens, M., and Pritchard, J. K. (2007). Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes.