STRUCTURE @ BioHPC

STRUCTURE is a free program 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 microsatellites, RFLPs and SNPs. The version currently installed at BioHPC is v2.2.3. For detailed description of the program and for literature references please consult the STRUCTURE web page.

Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.

This interface will launch the command-line version of STRUCTURE. Graphical front-end of STRUCTURE is currently not available. You will need to upload a data file and the parameters files mainparams and extraparams. The file mainparams must refer to the uploaded data file as input. Both input and output files referenced in mainparams must be in the current directory. File or path names starting with "/", "C:/", etc., are not allowed. Upon job completion, a gzipped tarball datafile_rslts.tgz of all input and output files will be available for ftp download via a link in a notification e-mail. Unless the "Maximum number of processors" (at the end of this page) is set to a value lower than the automatically supplied value, each instance (or "repetition") of the run will be executed on its own processor, concurrently with other instances. During the run, you will be able to monitor the log file (i.e., the standard output from the parallel driver program).

Please note: according to STRUCTURE developers, the bug which used to show up for small "lambda" and low allele frequencies has now been corrected in version 2.2.3 of the program, offered here. To facilitate cross-checks, we continue to support also the older version, 2.1 (see below).

The latest version (2.3.1), still in the beta-testing stage, is also supported.

E-mail:
(only guests need to use this field, registered users should log in)

Job name: (will be set to the name of data file)

Log file: (will be set after script file is selected)

Upload your data file
If your data file is larger than 10 MB, you can upload its compressed version (*.zip or *.gz). If the compressed version exceeds 35 MB, contact us.

Upload mainparams file
(the input/output files must be placed in the current directory and INFILE must be set to the name of the data file uploaded above)

Upload extraparams file
(if left blank, default parameters will be assumed)

Use program version 2.1 (old) 2.2.3 (new) 2.3.1 (beta!)

How many times to repeat the run?

Maximum number of processors to use
(lowering the number of processors may allow the job to start sooner, but it will increase the time of the calculation)

Cluster: ( Show timeout info )