Tree compatibility and inferring evolutionary history
Journal of Algorithms
On the approximability of numerical taxonomy (fitting distances by tree metrics)
Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms
Constructing Big Trees from Short Sequences
ICALP '97 Proceedings of the 24th International Colloquium on Automata, Languages and Programming
Inferring Evolutionary Trees with Strong Combinatorial Evidence
COCOON '97 Proceedings of the Third Annual International Conference on Computing and Combinatorics
COCOON '97 Proceedings of the Third Annual International Conference on Computing and Combinatorics
The Performance of Neighbor-Joining Algorithms of Phylogeny Recronstruction
COCOON '97 Proceedings of the Third Annual International Conference on Computing and Combinatorics
A few logs suffice to build (almost) all trees (I)
A few logs suffice to build (almost) all trees (I)
Absolute convergence: true trees from short sequences
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Zinc finger gene clusters and tandem gene duplication
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Estimating true evolutionary distances between genomes
STOC '01 Proceedings of the thirty-third annual ACM symposium on Theory of computing
Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Reconstructing optimal phylogenetic trees: a challenge in experimental algorithmics
Experimental algorithmics
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining
Journal of Algorithms - Special issue: Twelfth annual ACM-SIAM symposium on discrete algorithms
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A major computational problem in biology is the reconstruction of evolutionary trees for species sets, and accuracy is measured by comparing the topologies of the reconstructed tree and the model tree. One of the major debates in the field is whether large evolutionary trees can be even approximately accurately reconstructed from biomolecular sequences of realistically bounded lengths (up to about 2000 nucleotides) using standard techniques (polynomial-time distance methods, and heuristics for NP-hard optimization problems). Using both analytical and experimental techniques, we show that on large trees, the two most popular methods in systematic biology, Neighbor-Joining and Maximum Parsimony heuristics, as well as two promising methods introduced by theoretical computer scientists, are all likely to have significant errors in the topology reconstruction of the model tree. We also present a new general technique for combining outputs of different methods (thus producing hybrid methods), and show experimentally how one such hybrid method has better performance than its constituent parts.