Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond
The Bacillus cereus group, also known as B. cereus sensu lato (sl), is a species complex
that contains numerous closely related lineages, which vary in their ability to cause illness in …
that contains numerous closely related lineages, which vary in their ability to cause illness in …
Bayesian molecular dating: opening up the black box
Molecular dating analyses allow evolutionary timescales to be estimated from genetic data,
offering an unprecedented capacity for investigating the evolutionary past of all species …
offering an unprecedented capacity for investigating the evolutionary past of all species …
Predicting multiple conformations via sequence clustering and AlphaFold2
Abstract AlphaFold2 (ref.) has revolutionized structural biology by accurately predicting
single structures of proteins. However, a protein's biological function often depends on …
single structures of proteins. However, a protein's biological function often depends on …
ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models
ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular
tools for selecting the best-fit nucleotide and amino acid substitution models, respectively …
tools for selecting the best-fit nucleotide and amino acid substitution models, respectively …
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
J Trifinopoulos, LT Nguyen… - Nucleic acids …, 2016 - academic.oup.com
This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for
IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE …
IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE …
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Rapid growth of genome data provides opportunities for updating microbial evolutionary
relationships, but this is challenged by the discordant evolution of individual genes. Here we …
relationships, but this is challenged by the discordant evolution of individual genes. Here we …
ModelFinder: fast model selection for accurate phylogenetic estimates
Abstract Model-based molecular phylogenetics plays an important role in comparisons of
genomic data, and model selection is a key step in all such analyses. We present …
genomic data, and model selection is a key step in all such analyses. We present …
Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia
Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary
course of cancer. Chronic lymphocytic leukaemia (CLL) is a highly informative model for …
course of cancer. Chronic lymphocytic leukaemia (CLL) is a highly informative model for …
[HTML][HTML] Annelid functional genomics reveal the origins of bilaterian life cycles
Indirect development with an intermediate larva exists in all major animal lineages, which
makes larvae central to most scenarios of animal evolution,,,,,,,,–. Yet how larvae evolved …
makes larvae central to most scenarios of animal evolution,,,,,,,,–. Yet how larvae evolved …
Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista
F Burki, M Kaplan, DV Tikhonenkov… - … of the Royal …, 2016 - royalsocietypublishing.org
Assembling the global eukaryotic tree of life has long been a major effort of Biology. In
recent years, pushed by the new availability of genome-scale data for microbial eukaryotes …
recent years, pushed by the new availability of genome-scale data for microbial eukaryotes …