detectIR is a MATLAB-based tool for detecting both perfect inverted repeats and imperfect inverted repeats in DNA sequences. The manuscript describing the core algorithm of detectIR is published in PLOS ONE, 9(11):e113349.
This software is an open-source tool that follows the specifications of Creative Commons license (CC BY-NC-SA 3.0).
You can download the source codes and documents on this website, as well as on Sourceforge.net project websit.
In our publication, we did not conduct the comparison between IRF - Inverted Repeats Finder and detectIR because IRF cannot detect nested inverted repeats. We did do the comparison in our release (version 20141101). While IRF (version 3.05) can detect inverted repeats with indels in the pairing stem whereas detectIR cannot, detectIR shows much higher accuracy in detecting inverted repeats with mismatches within the pairing stem. Actually, based on the same HIV-1 genome, detectIR finds much more inverted repeats than IRF. Please see details after you download and unzip the file named detectIR.20150213.7z