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GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

Structure v. 2.3.3

Community rating: ?????

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

Quick Start

To use Structure v. 2.3.3, use the mainparams and extraparams found in the Community Data under structure
Resources: Structure Home page

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > structure

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

Input File(s)

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

Parameters Used in App

Enter 2 for the number of populations.

Output File(s)

Expect files named output_f, output_q and seed.txt. For the test case, the outputs file you will find in the example_data directory. The main file containing all information produced are in the output_f and can be used for further downstream analysis.

Tool Source for App

structure website at Pritchard group

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Structure v. 2.3.3 (archived)

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