Isolation by distance, web service - PubMed (original) (raw)

Isolation by distance, web service

Jeffrey L Jensen et al. BMC Genet. 2005.

Abstract

Background: The population genetic pattern known as "isolation by distance" results from spatially limited gene flow and is a commonly observed phenomenon in natural populations. However, few software programs exist for estimating the degree of isolation by distance among populations, and they tend not to be user-friendly.

Results: We have created Isolation by Distance Web Service (IBDWS) a user-friendly web interface for determining patterns of isolation by distance. Using this site, population geneticists can perform a variety of powerful statistical tests including Mantel tests, Reduced Major Axis (RMA) regression analysis, as well as calculate FST between all pairs of populations and perform basic summary statistics (e.g., heterozygosity). All statistical results, including publication-quality scatter plots in Postscript format, are returned rapidly to the user and can be easily downloaded.

Conclusion: IBDWS population genetics analysis software is hosted at http://phage.sdsu.edu/\~jensen/ and documentation is available at http://www.bio.sdsu.edu/pub/andy/IBD.html. The source code has been made available on Source Forge at http://sourceforge.net/projects/ibdws/.

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Figures

Figure 1

Figure 1

Example scatter plot. The plot was generated using the example raw allelic data and geographic information from the IBD.2 example data set available on the IBDWS website. The RMA regression line overlays the scatter plot. The plot was downloaded in postscript format from the website and slightly modified using Adobe Illustrator.

Figure 2

Figure 2

IBDWS example statistical results output. The figure shows a partial list of statistical output calculated from the IBD.2 sample data set. Results of Mantel tests and other calculations are also provided. All results can be downloaded as text files.

Figure 3

Figure 3

IBDWS forms interface. The figure shows a portion of the CGI web interface. Data can be uploaded from a text file using the Browse button or pasted directly into the form. Below the data input portion is a partial list of checkboxes for tailoring analyses. A total of twelve parameters are modifiable by the user.

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