Similarity index for genetic band profiles

Version 1.0.0.0 (2.91 KB) by Bram D'hondt
Calculates the similarity index for a given set of individual genetic band profiles.
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Updated 16 Mar 2012

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This script executes some basic calculations from the following article.

Leonard AC, Franson SE, Hertzberg VS, Smith MK & Toth GP (1999) Hypothesis testing with the similarity index. Molecular Ecology 8: 2105-2114.

Please consult this article for any conceptual or mathematical details.

The script calculates the mean similarity index (S) and its variance for a given set of individual genetic band profiles.

The input is a single matrix (*.txt) of which each row is a sample (genetic profile) and each column is a bin (genetic marker).

For example, the following data...

Markers: a b c d e f
Individual 1: 0 0 0 1 1 1
Individual 2: 0 0 1 0 1 0
Individual 3: 0 0 . . 0 0
Individual 4: 1 0 0 1 0 1

is entered as...

0 0 0 1 1 1
0 0 1 0 1 0
0 0 NaN NaN 0 0
1 0 0 1 0 1

and yields a mean S of 0.1778 and variance of 0.0316, when the script is run.

Cite As

Bram D'hondt (2024). Similarity index for genetic band profiles (https://www.mathworks.com/matlabcentral/fileexchange/35683-similarity-index-for-genetic-band-profiles), MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2011b
Compatible with any release
Platform Compatibility
Windows macOS Linux

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Version Published Release Notes
1.0.0.0