Phylogenetic tree building in the genomic age
Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …
Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis
Y Pan, L Wang, Z Feng, H Xu, F Li, Y Shen, D Zhang… - The lancet, 2023 - thelancet.com
Background Due to the national dynamic zero-COVID strategy in China, there were no
persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However …
persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However …
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
LT Nguyen, HA Schmidt… - … biology and evolution, 2015 - academic.oup.com
Large phylogenomics data sets require fast tree inference methods, especially for maximum-
likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find …
likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find …
RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language
Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite
of models. Consequently, users of these software packages are simultaneously forced to …
of models. Consequently, users of these software packages are simultaneously forced to …
Terrace aware data structure for phylogenomic inference from supermatrices
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix,
is commonly accompanied by the assumption of partition models. Under such models each …
is commonly accompanied by the assumption of partition models. Under such models each …
Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been
viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life …
viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life …
Data integration in Bayesian phylogenetics
Researchers studying the evolution of viral pathogens and other organisms increasingly
encounter and use large and complex data sets from multiple different sources. Statistical …
encounter and use large and complex data sets from multiple different sources. Statistical …
Using RAxML to infer phylogenies
A Stamatakis - Current protocols in bioinformatics, 2015 - Wiley Online Library
Inference of phylogenetic trees under the maximum likelihood (ML) criterion represents a
routine task in biological data analysis. In this unit we describe how to plan analyses and …
routine task in biological data analysis. In this unit we describe how to plan analyses and …
BEAGLE 3: improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics
BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The
BEAGLE library defines a simple, but flexible, application programming interface (API), and …
BEAGLE library defines a simple, but flexible, application programming interface (API), and …
Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets
The sizes of the data matrices assembled to resolve branches of the tree of life have
increased dramatically, motivating the development of programs for fast, yet accurate …
increased dramatically, motivating the development of programs for fast, yet accurate …