Characteristic Attribute Organization System
Indra Neil Sarkar, PhD, MLIS¹; Paul J. Planet, MD, PhD²; Rob DeSalle, PhD²
1. Center for Clinical and Translational Science, University of Vermont, Burlington, VT USA
2. Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA

In an ideal world, a full phylogenetic analysis would be done on every new sequence found. However, this is often a time 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. Phylogenomenclature (P-Gnome) is an implementation of the CAOS approach designed to approximate a parsimony-based tree analysis. 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 bifurcating 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.

System Requirements
The installers and Perl scripts are optimized for OS X (10.4.x PPC or Intel); however, they may be compiled for use on any other *NIX platform (including earlier versions of OS X). Source code can be downloaded from: http://phylogenomics.googlecode.com/svn/trunk/CAOS/

Downloading and Installing CAOS (P-Gnome & P-Elf)

1. Download the appropriate package:
• If you do not have BLAST installed (or are not sure*) [click here -- pgnomeXfull.mpkg.tgz ~35.9M].
  *you should consult your systems administrator to determine if you have BLAST installed.
• If you already have BLAST installed [click here -- pgnomeX.pkg.tgz ~180k].
• If you would like to download sample input files [click here -- pgnome_examples.tgz ~ 4k].
  • testSeqsTre.nex -- this is an example NON-INTERLEAVED MacClade File, containing both a matrix and a SINGLE tree
  • testSeqs.txt -- this is a test set file, in FASTA format (the seqs are the same as the input)
2. Uncompress the zip file.
   After you have downloaded the package -- if your browser has not already uncompressed the file -- double-click it, and this should automatically uncompress the package (.pkg or .mpkg file).
3. Double click the package file.
   This will install P-Gnome and P-Elf, the scripts for Phylogenomenclature.

Using CAOS
A manual consisting of download, installation, and usage instructions can be downloaded here: CAOS_Manual.pdf