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structure software

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The program structure is a free software package for using multi-locus genotype data to investigate population structure.

Quick Start

  • To use structure software, import your data in structure format which is a simple text file, Essentially, 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. The user can make several choices about format, and most of these data (apart from the genotypes!) are optional.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. Unless you plan to use the linkage model (see below) the order of the alleles for a single individual does not matter. The pre-genotype data columns (see below) are recorded twice for each individual. (More generally, for n-ploid organisms, data for each individual are stored in n consecutive rows unless the ONEROWPERIND option is used.). Alternatively, if data to be used are in another format please use PGDSpider to bring it to structure format
  • Resources: http://pritch.bsd.uchicago.edu/structure.html

Test Data

Info

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> structure

Input File(s)

Use file_for_analysis, mainparams and extraparams from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Use number of populations 2.

Output File(s)

Expect three files as an output. For the test case, the output files you will find in the example_data directory are named output_f, output_q and seed.txt The output_f file summarizes all information used as input parameters for the analysis of the data, like the arguments that would be used in the command line. Allele Frequency, overal proportion of membership of the samples, in the current test data, fit to two populations about the data under analysis as as well as the proportion each sample belongs to each of the two categories. The output_q contains only the proportion each sample belongs to one of the two groups.

Tool Source for App

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Include Page
docs:_DE_archived_apps_blurb
docs:_DE_archived_apps_blurb