Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023‏ - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Recent progress on reservoir history matching: a review

DS Oliver, Y Chen - Computational Geosciences, 2011‏ - Springer
History matching is a type of inverse problem in which observed reservoir behavior is used
to estimate reservoir model variables that caused the behavior. Obtaining even a single …

ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models

D Darriba, D Posada, AM Kozlov… - Molecular biology …, 2020‏ - academic.oup.com
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 …

[كتاب][B] Data integration, manipulation and visualization of phylogenetic trees

G Yu - 2022‏ - taylorfrancis.com
Data Integration, Manipulation and Visualization of Phylogenetic Trees introduces and
demonstrates data integration, manipulation and visualization of phylogenetic trees using a …

jModelTest: phylogenetic model averaging

D Posada - Molecular biology and evolution, 2008‏ - academic.oup.com
Abstract jModelTest is a new program for the statistical selection of models of nucleotide
substitution based on “Phyml”(. A simple, fast, and accurate algorithm to estimate large …

Relaxed phylogenetics and dating with confidence

AJ Drummond, SYW Ho, MJ Phillips, A Rambaut - PLoS biology, 2006‏ - journals.plos.org
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are
two extremes of a continuum. Despite their dominance in phylogenetic inference, it is …

High-throughput genomic data in systematics and phylogenetics

EM Lemmon, AR Lemmon - Annual Review of Ecology …, 2013‏ - annualreviews.org
High-throughput genomic sequencing is rapidly changing the field of phylogenetics by
decreasing the cost and increasing the quantity and rate of data collection by several orders …

[كتاب][B] Computational molecular evolution

Z Yang - 2006‏ - books.google.com
The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

Phylogenomics and the reconstruction of the tree of life

F Delsuc, H Brinkmann, H Philippe - Nature Reviews Genetics, 2005‏ - nature.com
As more complete genomes are sequenced, phylogenetic analysis is entering a new era—
that of phylogenomics. One branch of this expanding field aims to reconstruct the …

Time‐dependent rates of molecular evolution

SYW Ho, R Lanfear, L Bromham, MJ Phillips… - Molecular …, 2011‏ - Wiley Online Library
For over half a century, it has been known that the rate of morphological evolution appears
to vary with the time frame of measurement. Rates of microevolutionary change, measured …