Related papers: Gap-weighted subsequences for automatic cognate id…

Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…

Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…

Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…

To fully exploit the potential of computational phylogenetic methods for cognate data one needs to leverage specific (complex) models an machine learning-based techniques. However, both approaches require datasets that are substantially…

A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

Graphs provide a natural way to represent data by encoding information about objects and the relationships between them. With the ever-increasing amount of data collected and generated, locating specific patterns of relationships between…

Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…

Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…

Complete genome sequences contain valuable information about natural selection, but extracting this information for short, widely scattered noncoding elements remains a challenging problem. Here we introduce a new computational method for…

Sound correspondence patterns form the basis of cognate detection and phonological reconstruction in historical language comparison. Methods for the automatic inference of correspondence patterns from phonetically aligned cognate sets have…

Automatic phylogenetic inference plays an increasingly important role in computational historical linguistics. Most pertinent work is currently based on expert cognate judgments. This limits the scope of this approach to a small number of…

Cognates are variants of the same lexical form across different languages; for example 'fonema' in Spanish and 'phoneme' in English are cognates, both of which mean 'a unit of sound'. The task of automatic detection of cognates among any…

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…

The problem of inferring unknown graph edges from numerical data at a graph's nodes appears in many forms across machine learning. We study a version of this problem that arises in the field of \emph{landscape genetics}, where genetic…

Traditional classification tasks learn to assign samples to given classes based solely on sample features. This paradigm is evolving to include other sources of information, such as known relations between samples. Here we show that, even…

This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…

We show how field- and information theory can be used to quantify the relationship between genotype and phenotype in cases where phenotype is a continuous variable. Given a sample population of phenotype measurements, from various known…