dentearl/structureHarvester

Structure Harvester is a program for parsing the output of Pritchard's STRUCTURE and for performing the Evanno method.

Structure Harvester

(c) 2007-2022 The Author, see LICENSE for details.

Author

Dent Earl

Dependencies

• Python3

Installation

1. Download or clone the package.
2. Place structureHarvester.py and harvesterCore.py in the same directory (or leave them where they are).
3. There is no step 3.

Usage

Usage: structureHarvester.py --dir=path/to/dir/ --out=path/to/dir/ [options]

structureHarvester.py takes a STRUCTURE results directory (--dir) and an
output directory (--out will be created if it does not exist) and then
depending on the other options selected harvests data from the results
directory and performs the selected analyses

Options:
  --version         show program's version number and exit
  -h, --help        show this help message and exit
  --dir=RESULTSDIR  The structure Results/ directory.
  --out=OUTDIR      The out directory. If it does not exist, it will be created. Output written to summary.txt
  --evanno          If possible, performs the Evanno 2005 method. Written to evanno.txt. default=False
  --clumpp          Generates one K*.indfile for each value of K run, for use with CLUMPP. default=False

References

• J. Pritchard, M. Stephens, P. Donnelly. 2000. Genetics 155:945-959. http://pritch.bsd.uchicago.edu/structure.html http://www.genetics.org/cgi/content/full/155/2/945
• Evanno et al., 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14 , 2611 - 2620 http://www3.interscience.wiley.com/journal/118706173/abstract
• M. Jakobsson, N. Rosenberg 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14): 1801-1806. http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html http://bioinformatics.oxfordjournals.org/cgi/content/full/23/14/1801

Citation

• Earl, Dent A. and vonHoldt, Bridgett M. (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources vol. 4 (2) pp. 359-361. doi: 10.1007/s12686-011-9548-7 http://www.springerlink.com/content/jnn011511h415358/