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.
0.0
(0)
249 Downloads
Updated 16 Mar 2012

View License

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
Categories
Find more on Genomics and Next Generation Sequencing in Help Center and MATLAB Answers

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Version Published Release Notes
1.0.0.0