From HPC

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Revision as of 13:54, 8 January 2009

The program structure is a free software package for using multi-locus genotype data to investigate population structure. 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. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

http://pritch.bsd.uchicago.edu/structure.html

Command-line changes to parameter values

In order to simplify batch runs and make it easier to run simulations involving structure, we have added command-line flags that update the values of certain parameters, over-riding the values set in mainparams. These are as follows:

-m (mainparams) Read a different parameter input file instead of mainparams. 
-e (extraparams) Read a different parameter input file instead of extraparams. 
-s (stratparams) Read a different parameter input file instead of stratparams. (For use with the 
                   accompanying program, STRAT, for association mapping.) 
-K (MAXPOPS) Change the number of populations. 
-L (NUMLOCI) Change the number of loci. 
-N (NUMINDS) Change the number of individuals. 
-i (input file) Read data from a different input file. 
-o (output file) Print results to a different output file. 

Example

structure -K 5 -o output5