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Baltimore, September 2007

The SimPlot software, its documentation (including this document), the use of "SimPlot" in this context, and SimPlot icon copyright ã 1997-2007 Stuart C. Ray, M.D., All rights reserved

First, I want to thank:

Don Gilbert at Indiana University, who generously put the ReadSeq source code (ca. 1990) in the public domain. Dr. Gilbert who is responsible for how well file formats are detected. However, I am responsible for any bugs in the format detection, as I have changed the code significantly, e.g. adding detection of PHYLIP, Nexus, and other formats. 
The testers and users of SimPlot for helpful suggestions. In particular, Olav Hungnes and Mika Salminen's (long!) lists of requests have been an inspiration. 
Joe Felsenstein of the Department of Genetics at the University of Washington (Seattle), for making the PHYLIP suite excellent and freely available. Portions of PHYLIP version 3.5p have been incorportated into SimPlot with Dr. Felsenstein's permission.  He should not be held responsible for any problems with this code, since I might have introduced them.  If you have not already registered as a PHYLIP 3.5 user, please do so on his web site, available as a link under the Help menu in SimPlot.

If you share this program with others, please distribute the installer rather than just the executable, and please remind them to send me an email (see next paragraph). 

This program is "HelloWare". If you use it, please send me an email or letter saying so. A menu item to make this easy is included in the Help menu.  This program is NOT in the public domain, and may not be sold or distributed by anyone other than the author, nor may it be included in any collection of software (such as a CD-ROM) for distribution without the author's written consent.

If you find SimPlot useful and generate figures with it, whether for publication or presentation, I would appreciate acknowledgment since I provide this software without charge. A reference to the paper in which we first described SimPlot would also be nice:
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.


Please note this Disclaimer: This software is distributed "as is", with no warranty expressed or implied, and no guarantee for accuracy or applicability to any purpose.  So if it breaks your computer or distorts your results neither Johns Hopkins University nor I will not compensate you in any way. Even though I have made a reasonable effort to test this software, and even if I have been advised of errors in this software, the responsibility for use of this software rests solely with the user.  The validity of any results you obtain is your responsibility.  If you believe that any of the above is unreasonable or that any of the above entities should be liable then don't install or use this software or the contents of this installation file.

Before contacting me about a problem, please check the known problems section to make sure it is not already on the list.