The inference of gene trees with species trees
This article reviews the various models that have been used to describe the relationships
between gene trees and species trees. Molecular phylogeny has focused mainly on …
between gene trees and species trees. Molecular phylogeny has focused mainly on …
The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics
In the presence of recombination, the evolutionary relationships between a set of sampled
genomes cannot be described by a single genealogical tree. Instead, the genomes are …
genomes cannot be described by a single genealogical tree. Instead, the genomes are …
RASP 4: ancestral state reconstruction tool for multiple genes and characters
With the continual progress of sequencing techniques, genome-scale data are increasingly
used in phylogenetic studies. With more data from throughout the genome, the relationship …
used in phylogenetic studies. With more data from throughout the genome, the relationship …
Analysing recombination in nucleotide sequences
Throughout the living world, genetic recombination and nucleotide substitution are the
primary processes that create the genetic variation upon which natural selection acts. Just …
primary processes that create the genetic variation upon which natural selection acts. Just …
The role of recombination in the emergence of a complex and dynamic HIV epidemic
Background Inter-subtype recombinants dominate the HIV epidemics in three geographical
regions. To better understand the role of HIV recombinants in shaping the current HIV …
regions. To better understand the role of HIV recombinants in shaping the current HIV …
On the importance of assessing topological convergence in Bayesian phylogenetic inference
M Brusselmans, LM Carvalho, S L. Hong, J Gao… - Virus …, 2024 - academic.oup.com
Modern phylogenetics research is often performed within a Bayesian framework, using
sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the …
sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the …
[HTML][HTML] The era of the ARG: an empiricist's guide to ancestral recombination graphs
In the presence of recombination, the evolutionary relationships between a set of sampled
genomes cannot be described by a single genealogical tree. Instead, the genomes are …
genomes cannot be described by a single genealogical tree. Instead, the genomes are …
Computational tools for evaluating phylogenetic and hierarchical clustering trees
J Chakerian, S Holmes - Journal of Computational and Graphical …, 2012 - Taylor & Francis
Inferential summaries of tree estimates are useful in the setting of evolutionary biology,
where phylogenetic trees have been built from DNA data since the 1960s. In bioinformatics …
where phylogenetic trees have been built from DNA data since the 1960s. In bioinformatics …
Fidelity of hyperbolic space for Bayesian phylogenetic inference
Bayesian inference for phylogenetics is a gold standard for computing distributions of
phylogenies. However, Bayesian phylogenetics faces the challenging computational …
phylogenies. However, Bayesian phylogenetics faces the challenging computational …
A Bayesian supertree model for genome-wide species tree reconstruction
Current phylogenomic data sets highlight the need for species tree methods able to deal
with several sources of gene tree/species tree incongruence. At the same time, we need to …
with several sources of gene tree/species tree incongruence. At the same time, we need to …