SimPlot Download Page
updated June 6, 2005

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Welcome to my SimPlot download page. All of the software here is protected by copyright but free of charge. Before you download software you need to read my disclaimer.

This software is "Hello-ware". Please send me email if you download anything (note that you'll need to remove "nospam" from my email address). When you send that email, I would love to hear what organism(s) you are studying, and where you are located, though of course just "hello" would be fine. That way I can:

If you find SimPlot useful and generate figures with it, whether for publication or presentation, I would appreciate acknowledgment, such as a reference to the paper in which we first described SimPlot:

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1999 Jan;73(1):152-60.

NOTE: There was a bug in test versions 3.0-3.1, which were only distributed to a few users (whom I have contacted already). If you got hold of one of these versions indirectly, please contact me. The bug only affected bootscans when more than one bootscan was run in a session. The error was not always obvious, though it could generate bizarre results. Thank you to Una Smith of Los Alamos National Labs for reporting this problem!

Available for download (all are 32-bit applications for Microsoft Windows):

Simplot iconSimPlot software for detection and analysis of mosaic sequences
Here is a list of major changes, with details in the Help files. See Screen shots below (from version 2.5)

Version 3.4 beta (April 10, 2003)

Version 2.5 (March 18, 1999)

SimPlot version 2.5 - self-extracting ZIP archive (1.2 MB)
SimPlot version 2.5 - ZIP archive (1.2 MB)
Version 2.4 (March 5, 1999)
SimPlot version 2.4 - self-extracting ZIP archive (1.2 MB)
SimPlot version 2.4 - ZIP archive (1.2 MB)
version 1.3 (August 3, 1998)
SimPlot version 1.3 - ZIP archive (339 KB)
Version 1.3 was used in our recent publication:
Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, and Ray SC, "Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination" J Virol 1999; 73(1):152-160

Examples of output (quality reduced for WWW transmission): go to top

Similarity Plot:

Similarity plot
Diversity Plot:
Diversity plot

Where is SimPlot being used? go to top

Please let me know if your country is not listed.

Disclaimer: go to top

This software is supplied as-is, with no warranty of any kind expressed or implied. I have made a reasonable effort to avoid errors in design and execution of this software, but will not be liable for its use or misuse. The user is solely responsible for the validity of any results generated. Specifically, the author and his employer are not liable for any damage or data loss resulting from the use of this software, even if it is due to negligence on the part of the author of this software.

This software and this document are the responsibility of Stuart Ray, M.D. The views expressed herein do not necessarily represent the views of Johns Hopkins University.

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