Mutual relationships of human endogenous retroviruses (HERVs) and their similarities to other DNA elements are studied in this paper. We demonstrate that a completely data-driven grouping is able to reflect same kinds of relationships as more traditional biological classifications and phylogenetic taxonomies. The clusters and their visualization were computed with the Median Self-Organizing Map...

We present a method for hierarchical clustering of data called mutual information clustering (MIC) algorithm. It uses mutual information (MI) as a similarity measure and exploits its grouping property: The MI between three objects X, Y, and Z is equal to the sum of the MI between X and Y , plus the MI between Z and the combined object (XY ). We use this both in the Shannon (probabilistic) versi...

Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS show...

The molecular phylogeny of 24 Oecophylla smaragdina populations and two O. longinoda populations was studied using 647 bp of the mitochondrial cyt b gene. The phylogenetic analysis suggested that O. smaragdina and O. longinoda were separated from each other first, and after that the first within-species divergence of O. smaragdina occurred in early stage of their history, in which the Asian, Au...

Current brain-age prediction methods using magnetic resonance imaging (MRI) attempt to estimate the physiological brain age via some kind of machine learning of chronological brain age data to perform the classification task. Such a predictive approach imposes greater risk of either over-estimate or under-estimate, mainly due to limited training data. A new conceptual framework for more reliabl...

We present a method for hierarchical clustering of data called mutual information clustering (MIC) algorithm. It uses mutual information (MI) as a similarity measure and exploits its grouping property: The MI between three objects X, Y, and Z is equal to the sum of the MI between X and Y , plus the MI between Z and the combined object (XY ). We use this both in the Shannon (probabilistic) versi...

Abstract J. S. Bach’s Well-Tempered Clavier II is well known for the complexity of its source situation, and vast array variant readings. The current article uses techniques phylogenetic analysis, developed in biological sciences, to deepen our understanding complex relationships between primary sources. computer algorithm NeighborNet used analyse data comprising textual variants Prelude A, bwv...

Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavil...