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The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal “DNA barcode” for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses h ...
Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so t ...
A fundamental requirement of quantitative palaeoecology is consistent taxonomy between a modern training set and palaeoecological data. In this study we assess the possible consequences of violation of this requirement by simulating taxonomic errors in tes ...
Background: Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve the inference of regulatory networks for ...
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0
Background: Reassortments are events in the evolution of the genome of influenza (flu), whereby segments of the genome are exchanged between different strains. As reassortments have been implicated in major human pandemics of the last century, their identi ...
Background: Reassortments are events in the evolution of the genome of influenza (flu), whereby segments of the genome are exchanged between different strains. As reassortments have been implicated in major human pandemics of the last century, their identi ...
The study of genorne rearrangement is much harder than the corresponding problems on DNA and protein sequences, because of the occurrences of numerous combinatorial structures. By explicitly exploring these combinatorial structures, the recently developed ...
The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...
Marine and freshwater ecosystems are fundamentally different regarding many biotic and abiotic parameters. The physiological adaptations required for an organism to pass the salinity barrier are considerable. Many eukaryotic lineages are restricted to eith ...
