Neighbor joining algorithms for inferring phylogenies via LCA-distances
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| Description: |
Moran, S (Israel)
Thursday 06 September 2007, 10:20-10:40 PLGw01 - Current Challenges and Problems in Phylogenetics |
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| Created: | 2007-09-24 10:25 | ||
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| Collection: | Phylogenetics | ||
| Publisher: | Isaac Newton Institute | ||
| Copyright: | Moran, S | ||
| Language: | eng (English) | ||
| Distribution: |
World
(downloadable)
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| Credits: |
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| Explicit content: | No | ||
| Aspect Ratio: | 4:3 | ||
| Screencast: | No | ||
| Bumper: | /sms-ingest/static/new-4x3-bumper.dv | ||
| Trailer: | /sms-ingest/static/new-4x3-trailer.dv | ||
| Abstract: | Reconstructing phylogenetic trees efficiently and accurately from distance estimates is an ongoing challenge in computational biology from both practical and theoretical considerations. We study algorithms which are based on a characterization of edge-weighted trees by distances to LCAs ({\em Least Common Ancestors}). This characterization enables a direct application of ultrametric reconstruction techniques to trees which are not necessarily ultrametric. A simple and natural neighbor joining criterion based on this observation is used to provide a family of efficient neighbor-joining algorithms. These algorithms are shown to reconstruct a refinement of the Buneman tree, which implies optimal robustness to noise under criteria defined by Atteson. In this sense, they outperform many popular algorithms such as Saitou\&Nei's NJ. Preliminary experimental results indicate that when executed from an appropriate root taxon, this algorithm provides reconstruction of phylogenies which are competitive with NJ and other common algorithms. |
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