In order to understand the population structure and dynamics of bacterial microorganisms, typing systems that accurately reflect the phylogenetic and evolutionary relationship of the agents are required. Over the past 15 years multilocus sequence typing schemes have replaced single locus approaches, giving novel insights into phylogenetic and evolutionary relationships of many bacterial species...

Bioinformatics experiments are rapidly evolving with genomic projects that analyze large amounts of data. This fact demands high performance computation and opens up for exploring new approaches to provide better control and performance when running experiments, including Phylogeny/Phylogenomics. We designed a phylogenetic scientific workflow, named SciPhy, to construct phylogenetic trees from ...

I. Types of Molecular Data: Certainly the lion’s share of molecular data used in phylogeny estimation in is DNA sequence data, but we should examine other types of molecular data, and some of the characteristics of those data that influence phylogeny estimation. A. Inherently Distance-based Data As I indicated last week, there are molecular phylogenetic approaches in which the nature of the dat...

MOTIVATION Most existing approaches for phylogenetic inference use multiple alignment of sequences and assume some sort of an evolutionary model. The multiple alignment strategy does not work for all types of data, e.g. whole genome phylogeny, and the evolutionary models may not always be correct. We propose a new sequence distance measure based on the relative information between the sequences...

The use of diverse data sets in phylogenetic studies aiming for understanding evolutionary histories species can yield conflicting inference. Phylogenetic conflicts observed animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we used target enrichment data, tree, network approaches to infer the backbone phylog...

Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multipl...

Background: Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results: TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004) are described. TREEFINDER is written in ANSI C ...

Maximum parsimony and maximum likelihood are two contrasting approaches for reconstructing phylogenetic trees from sequence and character data. We establish analytic links between these methods (extending connections reported earlier) under the simple Poisson model of substitutions in two settings. First, we show that if the underlying state space is sufficiently large then the maximum likeliho...

In this paper we consider the neuroscienti€c theory of the Bayesian brain in the light of adaptive web systems and content personalisation. In particular, we elaborate on neural mechanisms of human decision-making and the origin of lacking reliability of user feedback, o‰en denoted as noise or human uncertainty. To this end, we €rst introduce an adaptive model of cognitive agency in which popul...

The brain uses sensory information that is often uncertain in order to efficiently generate perceptual representations of the world. This observation has led to the Bayesian brain hypothesis, in which the brain combines internal expectations of the world with unreliable external sensory information in a nearly optimal probabilistic manner. Recent studies have suggested that to be true in statis...