Phylogenetic trees are tree structures that depict relationships between organisms. Popular analysis techniques often produce large collections of hypothetical trees, which can be expensive to store. This can also make the exchange of such data also difficult. TreeZip compresses phylogenetic trees based on the shared evolutionary relationships. In our experiments, TreeZip has been shown to be very effective, typically compressing a tree file to less than 2% of its original size. When coupled with standard compression methods such as 7zip, TreeZip can compress a file to less than 1% of its original size.

TreeZip 2.0

TreeZip 2.0 is now available for download! It has several important updates from TreeZip 1.0.

• Support for weighted phylogenetic trees.
• A flexible decompressor that allows you to extract sub-collections of trees of interest (all the trees, a random number, or the set of unique trees)
• Set Operations: Perform set operations such as union, intersection, set difference and equivalence -- directly on the compressed TRZ file! No need to decompress!
• Compute Consensus: Strict and majority consensus trees can be extracted directly from the compressed TRZ file. Again, there is no need to decompress!

Funding for TreeZip was supported by the National Science Foundation under grants DEB-0629849, IIS-0713168, and IIS-1018785.

To Cite:

Matthews SJ, Williams TL. An efficient and extensible approach for compressing phylogenetic trees. BMC Bioinformatics 12(Suppl 10), volume 12, S16, 2011. link

Matthews SJ, Sul S, and Williams TL. A Novel Approach for Compressing Phylogenetic Trees. Bioinformatics Research and Applications, pp. 113 – 124, 2010.link