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downloads | disclaimer

Welcome to the CleanCollapse page. CleanCollapse is protected by copyright but free of charge. Before you download software you need to read my disclaimer (below).

This software is "Hello-ware". When you register on the download server, all you have to provide is a valid email address, but I would love to hear what organism(s) you are studying, and where you are located. The email address allows me to:

CleanCollapse is a relatively user-friendly Windows program that accepts an alignment of sequences, and optionally can remove rare sporadic polymorphisms that may represent analytical artifacts, and also reduce redundancy by "collapsing" identical sequences into a single sequence. The program provides a record of these manipulation, and some rudimentary analysis (e.g. proportion of synonymous and nonsynonymous sporadic changes) that may assist interpretation.

The program (as well as its icon and name) is protected by copyright but is distributed free of charge. Please do not give it to others - just send them here so that I can get some indication of how and where the software is being used. This helps me prioritize projects, prioritize enhancements, and notify users when a new release is available.


I am indebted to Don Gilbert, who placed the ReadSeq code in the public domain. CleanCollapse contains a heavily modified version of the Pascal source, circa 1990. I added recognition of Phylip (interleaved and sequential), PAUP/Nexus, MSF, and a few others - so any bugs are my fault.

The rationale for calculating the frequency of sporadic changes, and questions about the validity of ascribing viral diversity to them, are described in an excellent paper: Smith DB, McAllister J, Casino C, Simmonds P. Virus 'quasispecies': making a mountain out of a molehill? J Gen Virol 1997 Jul; 78: 1511-9.

Downloads and version history

To obtain CleanCollapse: click this link to the download server. If the download server is not working, just write me an email message (address below) and I will kick the server.

Version 1.0.5 (May 2006) download (4.4 MB), which contains minor improvements

Version 1.0.2 (June 2005) download (4.4 MB) was the first version to be distributed beyond close colleagues.


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. [Note to human correspondents - you will need to remove "nospam" from this email address for it to work. My hope is that automated readers (spam factories) won't notice.]

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