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

README.md

Structure Harvester

(c) 2007-2014 The Author, see LICENSE for details.

Author

Dent Earl

Dependencies

  • Python version 2.5 < x < 3.0

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

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/
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