Download Algorithms in Bioinformatics: 12th International Workshop, by Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao (auth.), Ben PDF

By Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao (auth.), Ben Raphael, Jijun Tang (eds.)

This e-book constitutes the refereed court cases of the twelfth foreign Workshop on Algorithms in Bioinformatics, WABI 2012, held in Ljubljana, Slovenia, in September 2012. WABI 2012 is certainly one of six workshops which, in addition to the eu Symposium on Algorithms (ESA), represent the ALGO annual assembly and makes a speciality of algorithmic advances in bioinformatics, computational biology, and platforms biology with a selected emphasis on discrete algorithms and machine-learning tools that tackle very important difficulties in molecular biology. The 35 complete papers offered have been conscientiously reviewed and chosen from ninety two submissions. The papers contain algorithms for quite a few organic difficulties together with phylogeny, DNA and RNA sequencing and research, protein constitution, and others.

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Extra info for Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings

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C Springer-Verlag Berlin Heidelberg 2012 Efficient Computation of Popular Phylogenetic Tree Measures 31 unique evolutionary histories, and are therefore important conservation targets. Phylogenetic relationships among species can be used to understand biogeographic patterns [9], to infer processes underlying local community assembly [2] and to inform conservation decision making [3]. Given a particular phylogenetic tree T , many measures have been proposed to describe the phylogenetic composition of a set of tips, that is a set of leaf nodes of the tree that represent the finest taxonomic unit in the analysis (for example animal species, languages etcetera).

1 Introduction Background and Motivation. Ecologists are increasingly using information on phylogenetic relationships among species to gain new insights into both fundamental and applied questions. This is motivated in part by the observation that closely related species often share similar phenotypic and ecological characteristics. Species with high phylogenetic distinctiveness also represent particularly Center for Massive Data Algorithmics, a Center of the Danish National Research Foundation.

We denote this quantity by T C(e), thus: T C(e) = cost(u, v). {u,v}∈Δ(S) e∈p(u,v) It is easy to show that the latter quantity can be expressed as follows: T C(e) = (s − s(e)) wl · s(l) + s(e) l∈Off(e) = (s − s(e)) wl · s(l) + s(e) l∈Off(e) e∈E wl · s(l) l∈Ind(e) wl · (s − s(l)) (5) l∈Anc(e) wl · s(l) − + s(e) wl · (s − s(l)) + s(e) l∈Anc(e) wl · s(l) Off(e)∪Anc(e) For a node u that is a tip of T , we define the total path cost of u as the sum of the costs of all simple paths between u and any other tip of T .

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