EvoZip: Efficient Compression of Large Collections of Evolutionary Trees

TL;DR

EvoZip is a new phylogenetic tree compression method that significantly outperforms the current state-of-the-art in compression ratio and speed, enabling more efficient storage and retrieval of large tree collections.

Contribution

EvoZip introduces novel encoding schemes and compression techniques that improve upon TreeZip for phylogenetic tree compression.

Findings

71.6% better compression on average

80.71% less compression time

60.47% less decompression time

Abstract

Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a common leafset. Storing and sharing such large collection of trees requires considerable amount of space and bandwidth. Furthermore, the huge size of phylogenetic tree databases can make search and retrieval operations time-consuming. Phylogenetic compression techniques are specialized compression techniques that exploit redundant topological information to achieve better compression of phylogenetic trees. Here, we present EvoZip, a new approach for phylogenetic tree compression. On average, EvoZip achieves 71.6% better compression and takes 80.71% less compression time and 60.47% less decompression time than TreeZip, the current state-of-the-art algorithm for phylogenetic tree compression. While EvoZip is based on TreeZip, it betters TreeZip due to (a) an improved bipartition and support list encoding scheme, (b) use of Deflate compression algorithm, and (c) use of an efficient tree reconstruction algorithm. EvoZip is freely available online for use by the scientific community.