Structure
Overview
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.
Restrictions on use
All users may access and use Structure.
The appropriate citation for the basic method is to Pritchard et al. (2000a). The paper by Falush
et al. (2003a) is the appropriate reference for the linkage model and the correlated allele frequencies
model implemented in Version 2.0. The methods for ambiguous genotype data such as dominant
markers (new in Version 2.2) are described by Falush et al. (2007). The models of informative priors
for small data sets (new in Version 2.3) is described by Hubisz et al. (2009).
Set up procedure
Your input file should be of the format:
Running the application
Please do not run Structure commands on the login node. qrsh is recommended for some commands. Computationally intense work should be done via the batch system.
Command line arguments available are:
-m mainparams
-e extraparams
-s stratparams
-K MAXPOPS
-L NUMLOCI
-N NUMINDS
-i input file
-o output file
-D SEED
Examples
The following example first runs structure as a serial job.
#!/bin/bash --login #$ -S /bin/bash #$ -cwd module load apps/intel-17.0/structure/2.3.4 structure -m mainparams -e extraparams -i testdata1
and submit the job using qsub jobscript where jobscript is the name of your job script file.