CDTree's Expanding Canopy:  
New Growth for CDD's Software Tool for Conserved Domain Hierarchies

The increasing number of conserved domains (CDs) curated by the Structure Group
for the Conserved Domain Database (CDD) naturally leads to the exploration of
relationships among the CDs.  CDTree is a software tool designed to create,
investigate, maintain and record hierarchical relationships among CDs in a consistent, 
coherent fashion.  Parent-child relationships within a family are to be
established based on related biological function and strong evidence of an
evolutionary link, using the structure-based multiple alignments developed for
each CD, auxiliary biological data sources and guided by the expertise of the CDD curators. 

CDTree enables the CDD curation team to build CD hierarchies efficiently by
assembling a powerful suite of tools to examine CDs singly and collectively.
Among CDTree's capabilities are:

  *  hierarchy & individual CD creation and manipulation
  *  non-redundification of sequences in CDs
  *  compute sequence trees based on one or more CD's member sequences
     using various distance measures and tree algorithms
  *  a browsable taxonomy tree to show a CD's taxonomic spread
  *  domain architecture information obtained from CDART
  *  BLAST-derived cross- and self-recognition scores for CDs
  *  two-way communication with Cn3D when editing family members

In this quadrennial review presentation, I present an overview of the newest
version of the CDTree software after a summary of prior work.  I will
highlight CDTree components with which I have been most involved (hierarchy
validation, sequence tree algorithms and a viewer on CDART data) and close with
a short demonstration.