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Fast Reconstruction of Large Phylogenetic Trees Using Iterative DCM3 Technique

This presentation introduces a novel algorithmic approach called Iterative DCM3, which utilizes a divide-and-conquer strategy to enhance the efficiency of maximum parsimony (MP) heuristics for reconstructing large phylogenetic trees. We compare this new technique against existing MP heuristics using real biological datasets. The iterative process includes local search optimizations, DCM3-decomposition, and random tree refining. Our experiments demonstrate that I-DCM3(Ratchet) significantly outperforms traditional Ratchet methods, especially on larger datasets, indicating a fruitful direction for future research.

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Fast Reconstruction of Large Phylogenetic Trees Using Iterative DCM3 Technique

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  1. Iterative-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees Usman Roshan and Tandy Warnow U. of Texas at Austin Bernard Moret and Tiffani Williams U. of New Mexico

  2. This talk • New technique, based upon a particular divide-and-conquer strategy (DCM3), for speeding up heuristics for MP • Comparison against current MP heuristics on real datasets • Future research

  3. DCM3 Decompositions Input: Set S of sequences, and guide-tree T 1. Compute “short subtree” graph G(S,T), based upon T 2. Find clique separator in the graph G(S,T), and form subproblems

  4. New technique: Iterative DCM3 Repeat: 1. Apply TBR-based local search till a local optimum is reached. 2. Obtain a DCM3-decomposition based upon the local optimum (the “guide tree” ). 3. Apply base method to subproblems, and merge subtrees using the Strict Consensus Merger. 4. Randomly refine the tree. Variants we have examined: I-DCM3(TBR) and I-DCM3(Ratchet).

  5. Comparison of MP heuristics • Methods: TBR search, Ratchet, I-DCM3(TBR), I-DCM3(Ratchet) • Datasets: Biological data • Experimental Methodology: • On each dataset we ran 10 trials of each method (each trial for 24 hours). • We then plotted avg. best MP scores after fixed time intervals. • Implementation: Ratchet was implemented using PAUP*4.0 and I-DCM3 was implemented by us using C++. We used Linux Pentium machines for our experiments.

  6. 2000 Eukaryotes sRNA (Gutell et. al.)

  7. 2594 rbcL DNA (Kallersjo et. al.)

  8. Conclusions • I-DCM3(Ratchet) finds best known trees faster than Ratchet. • On larger trees the improvement of I-DCM3 (Ratchet) over Ratchet is more pronounced. Out of 10 trials, on the two largest datasets, best I-DCM3(Ratchet) tree is 9 and 7 steps better then best Ratchet tree

  9. Future work • Use recursive I-DCM3 for analyzing very large datasets • Biological analysis of real datasets • Use I-DCM3 for boosting ML heuristics

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