CleanCollapse is a relatively user-friendly Windows program that takes 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.
SCRoftware* Home page
The links at left provide access to software developed by Stuart Ray for analysis of microbial sequences.
These links will ultimately lead you to a download server, which will prompt you for your email address, to which your download password will be sent. Your email address will NOT be used for any marketing or shared with any commercial entity - it's just so that I can let you know if there are bugs or updates related to the software you have downloaded.
These programs run only under Microsoft Windows (2000 and XP, at least). Users have told me that they work fine under emulators of Windows running on other platforms, but your mileage may vary.
Vista users: the software below should run on Windows Vista, but the Help files will not open unless you have installed the Microsoft Windows Help viewer program (free).
Marginal Frequencies: Simply automates a tedious process - generating a table of variability for each site in an alignment. This program accepts sequence alignments in many different formats. It also does some rudimentary analysis for covariation.
Phylogenetic analysis made a little easier. This program accepts sequence alignments in many different formats, and makes it easy to generate a tree using PHYLIP or PAUP* (if available on the workstation).
Similarity Plotting (as well as bootscanning, quick tree generation, and informative-sites analysis): A popular tool for recombination analysis (used in more than 850 publications [Acrobat PDF])
Variability Plot: Sliding-window analysis of genetic distances among sequences. Includes Nei-Gojobori model for nonsynonymous distance. This program accepts sequence alignments in many different formats.
Visual Signature Pattern Analysis via a user-friendly Windows program that accepts an alignment of sequences, interactively analyzes frequencies of residues at each position in groups of sequences and supports the generation of sequence logos. The frequency calculations and program name were inspired by VESPA (by Gerry Myers and Bette Korber of Los Alamos National Labs). The logos were inspired by the work of Tom Schneider (of NCI) and Jan Gorodkin and colleagues (DTU, Denmark)..
Not because it sounds great. Basically, it starts with my initials and rhymes with "software", and I was pretty sure that it wasn't already taken. That latter part is important for Windows installers, so that I don't try to install software into someone else's directory tree. Since I don't need a catchy name for a non-profit operation, who cares?