Quartet-Based Phylogeny Reconstruction from Gene Orders

Abstract. Phylogenetic reconstruction from gene-rearrangement data is attracting increasing attention from biologists and computer scientists. Methods used in reconstruction include distance-based methods, parsimony methods using sequence encodings, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach; however, its exhaustive approach means that it can be applied only to small datasets of fewer than 15 taxa. While we have successfully scaled it up to 1,000 genomes by integrating it with a disk-covering method (DCM-GRAPPA), the recursive decomposition may need many levels of recursion to handle datasets with 1,000 or more genomes. We thus investigated quartet-based approaches, which directly decompose the datasets into subsets of four taxa each; such approaches have been well studied for sequence data, but not for gene-rearrangement data. We give an optimization algorithm for the NP-hard problem of com...

• Type: Conference
• Year: 2005
• Where: COCOON
• Authors: Tao Liu, Jijun Tang, Bernard M. E. Moret
• Keywords: COCOON 2005, Distance-based Methods, Gene-rearrangement Data, Software Suite Grappa