T - Tree , a new tool for taxonomy - based phylogenetic co - evolution analysis

Cladograms are dendrograms (tree-shaped diagrams) of proteins that are easily constructed by automated tools using phylogenetic techniques such as the tool ClustalW. Cladograms correspond to evolutionary relationships, but they are not easily projected onto actual consensus taxonomies. This paper describes T-Tree, an original application that maps bioinformatic-tool generated phylogenetic cladograms (such as those generated by ClustalW) onto taxonomic trees. T-Tree also provides a structure for performing additional phylogenetic analysis including filtering, data conditioning, and utilizing additional new statistical tools for detecting congruence between trees. T-Tree results provide a cognitive framework for hypothesizing whether candidate sets of molecules are co-evolutionary, an important test for many investigations. If the cardinality of the tree is sufficient, T-Tree utilizes DeVienne's new Icong tree congruence tool for analyzing co-evolutionary relationships. This paper presents the results from applying T-Tree to data sets of nuclear hormone receptor PPAR Gamma and its ligand, Insulin. This work demonstrates how the TTree tool could be used to explore general co-evolutionary relationships between sets of evolving molecules including proteins and nucleic acids.