A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance

Phylogenetic tree searching algorithms often produce thousands of trees which biologists save in Newick format in order to perform further analysis. Unfortunately, Newick is neither space efficient, nor conducive to post-tree analysis such as consensus. We propose a new format for storing phylogenetic trees that significantly reduces storage requirements while continuing to allow the trees to be used as input to post-tree analysis. We implemented mechanisms to read and write such data from and to files, and also implemented a consensus algorithm that is faster by an order of magnitude than standard phylogenetic analysis tools. We demonstrate our results on a collection of data files produced from both maximum parsimony tree searches and Bayesian methods.

• Type: Conference
• Year: 2005
• Where: WABI
• Authors: Robert S. Boyer, Warren A. Hunt Jr., Serita M. Nelesen
• Keywords: Algorithms, Phylogenetic Trees, Post-tree Analysis, Tree Searching Algorithms, WABI 2005