In an ideal world, a full phylogenetic analysis would be done on every new sequence found. However, this is often a time-consuming and computer-intensive task. The Characteristic Attribute Organization System (CAOS) is an algorithm to discover descriptive information about a priori organized discretized data (e.g., from a phylogenetic analysis). Derived from some of the fundamental tenets from evolutionary biology, rule sets can be generated from data sets that can be used for effecicient and effective classification of novel data elements. It important to emphasize that CAOS is NOT a tree analysis, instead it is a classification scheme based on a phylogenetic analysis. Based on information (rules) discovered from the phylogenetic analysis that unambiguously distinguish between each node on a tree, CAOS is able to classify novel sequences. Studies have indicated that CAOS-based classification has over a 95% accuracy rate of classification, as determined by where sequences would be classified if a full phylogenetic analysis were to be done using the novel and known sequences. Publications about CAOS as well as those citing or using CAOS can be found here.
RubyCAOS is an implementation of the CAOS approach designed to approximate a parsimony-based tree analysis. The software tool for computes diagnostic character states from phylogenetic trees and uses them for classification of new molecular sequences. RubyCAOS is a platform independent version of the same algorithm that was orginally written in Perl and C++. This tool is freely available and can be used as both a standalone application as well as a class library.
A Web version enables simple-based CAOS procedures (single character positions), either for only extracting diagnostics or for classification of new sequences.
RubyCAOS requires Ruby (1.8+ or 1.9.1+), which is installed on most *NIX based machines. The installation scripts and tools have been developed and tested for Mac OS X 10.6+ and Linux. The application requires BLAST 2.2.23 and the BioRuby gem ('bio'). Mac OS X users can use the single click installer below to install BLAST, the BioRuby gem, and RubyCAOS. Full details about installation requirements can be found in the "Readme.txt" file in the download.
Download and Install RubyCAOS
Option 1 (full source): The full source code and installation scripts are designed for most *NIX environments (including Linux and OS X 10.6+). Within the zip file, there is a README.txt file that contains installation instructions.
The file can be obtained here: RubyCAOS.zip
Option 2 (OS X w/BLAST): For Mac OS X (10.6+) users, the following double-click installer can also be used (180MB download, which includes an installation of BLAST+): OSX_rubyCAOS.dmg
Option 3 (Web-CGI): For those wishing to develop a customized Web version of CAOS, the source code for the CGI based Web version of RubyCAOS can also be downloaded: WebCAOS.zip
Thanks to all who have contributed to CAOS over the years!
Gratitude is given to all who have contributed to the design and development of CAOS since the beginning.
Especially Dr. Paul J. Planet, Dr. Rob DeSalle, and Dr. David Figurski who contributed to the original development of the CAOS algorithm. Additional thanks to Dr. Bernd Schierwater, Dr. Heike Hadrys, Dr. Joseph Thornton as well as our community of users worldwide who continue to use and make suggestions for future improvements.
CAOS is a Columbia University Patented Technology:
International Patent Number: WO 02/064813 A2; United States Patent Number: PCT/US02/03540; United States Priority Number: 60/267,972