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Concept

Distance matrices in phylogeny

Related publications (11)

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Spatiotemporal wildfire modeling through point processes with moderate and extreme marks

Jonathan Koh Boon Han

Accurate spatiotemporal modeling of conditions leading to moderate and large wildfires provides better understanding of mechanisms driving fire-prone ecosystems and improves risk management. Here, we develop a joint model for the occurrence intensity and t ...

2023

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Jacques Fellay

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical opti ...

OXFORD UNIV PRESS2022

Study of cell differentiation by phylogenetic analysis using histone modification data

Bernard Moret, Philipp Bucher, Yu Lin, Nishanth Ulhas Nair

Background: In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in ...

BioMed Central2014

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

Bernard Moret, Yu Lin, Vaibhav Rajan

TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, ...

Oxford University Press2012

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Yu Lin, Vaibhav Rajan

Background: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have be ...

BioMed Central2012

Analysis of Co-evolving Gene Families Using Mutually Exclusive Orthologous Modules

Xiuwei Zhang

Coevolutionary networks can encapsulate information about the dynamics of presence and absence of gene families in organisms. Analysis of such networks should reveal fundamental principles underlying the evolution of cellular systems and the functionality ...

2011

Spatial modelling of extreme snow depth

Anthony Christopher Davison, Juliette Ferial Blanchet

The spatial modelling of extreme snow is important for adequate risk management in Alpine and high altitude countries. A natural approach to such modelling is through the theory of max-stable processes, an infinite-dimensional extension of multivariate ext ...

2011

Is There a Size Limit for Cosmopolitan Distribution in Free-Living Microorganisms? A Biogeographical Analysis of Testate Amoebae from Polar Areas

Jiangyan Yang

A long-standing debate in microbial ecology is the extent to which free-living microorganisms exhibit cosmopolitan distributions. We use a comparison of testate amoebae communities in cold "polar" locations (Arctic, Antarctic, and Tibet) to investigate how ...

Springer-Verlag2010

On Exploring Genome Rearrangement Phylogenetic Patterns

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 ...

Springer-Verlag New York2010

Ribosomal RNA Genes Challenge the Monophyly of the Hyalospheniidae (Amoebozoa: Arcellinida)

Enrique Lara

To date only five partial and two complete SSU rRNA gene sequences are available for the lobose testate amoebae (Arcellinida). Consequently, the phylogenetic relationships among taxa and the definition of species are still largely dependant on morphologica ...

2008