Algorithms in Bioinformatics: 11th International Workshop, by Broňa Brejová, Michal Burger, Tomáš Vinař (auth.), Teresa M.

By Broňa Brejová, Michal Burger, Tomáš Vinař (auth.), Teresa M. Przytycka, Marie-France Sagot (eds.)

This ebook constitutes the refereed court cases of the eleventh foreign Workshop on Algorithms in Bioinformatics, WABI 2011, held in Saarbrücken, Germany, in September 2011.
The 30 papers provided have been rigorously reviewed and chosen from seventy seven submissions. They disguise features of algorithms in bioinformatics, computational biology and structures biology.

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Extra info for Algorithms in Bioinformatics: 11th International Workshop, WABI 2011, Saarbrücken, Germany, September 5-7, 2011. Proceedings

Example text

We capture the sequence s of heterozygous loci used in (2) by binary variables bi,p,q , which indicate a maximal block of homozygous loci between heterozygous loci p and q in genotype i: q−1 bi,p,q = a ˜i,p · a ˜i,q · (1 − a ˜i,r ) 1 ≤ i ≤ L, 1 ≤ p < q ≤ m (9) r=p+1 To formulate the probability given in (2), let ξkj denote the event of obtaining a chromosome k from a genotype j. Using variables h, b, and z, we can express Pr[ ξkj ] such that in the heterozygous case every maximal homozygous block contributes rp,q if it contains at least one crossover, and (1 − rp,q ) otherwise.

Short quartet puzzling: A new quartet-based phylogeny reconstruction algorithm. J. Comp. Biol. 15(1), 91–103 (2008) 17. : Scoredist: A simple and robust protein sequence distance estimator. BMC Bioinf. 6, 108 (2005) 18. : Bayesian probabilities and quartet puzzling. Mol. Biol. Evol. 14(2), 210–211 (1996) 19. : Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13(7), 964–969 (1996) 20. : Large-scale neighbor-joining with NINJA. , Warnow, T.

On the complexity of distance-based evolutionary tree reconstruction. In: Proceedings of SODA 2003, pp. 444–453 (2003) Towards a Practical O(n log n) Phylogeny Algorithm 25 14. : FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26(7), 1641– 1650 (2009) 15. : Quartet-based phylogenetic inference: Improvements and limits. Mol. Biol. Evol. 18(6), 1103–1116 (2001) 16. : Short quartet puzzling: A new quartet-based phylogeny reconstruction algorithm.

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