Phylogenetic hypotheses

Ebook "Introduction to computational biology: An evolutionary approach" Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models.

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Understanding disjunct distribution patterns in the Balkan Peninsula and Anatolia is important in order to reconstruct robust biogeographical hypotheses. This is instrumental in understanding the recolonization patterns of Europe during the Quaternary glaciation/interglaciation periods and the potential role of Anatolia as a refugium. Unfortunately, only a few studies have been conducted to uncover such processes. Here, we used all eight species of the genus Bornmuellera (Brassicaceae) with a scattered distribution in the Balkans and Anatolia to reconstruct its biogeographic history.

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Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts.

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We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees.

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Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria.

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