The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method

JM Miller, CI Cullingham, RM Peery - Heredity, 2020 - nature.com
Inference of genetic clusters is a key aim of population genetics, sparking development of
numerous analytical methods. Within these, there is a conceptual divide between finding de …

PAML 4: phylogenetic analysis by maximum likelihood

Z Yang - Molecular biology and evolution, 2007 - academic.oup.com
Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of
DNA and protein sequences using maximum likelihood (ML). The programs may be used to …

The interrelationships of land plants and the nature of the ancestral embryophyte

MN Puttick, JL Morris, TA Williams, CJ Cox, D Edwards… - Current Biology, 2018 - cell.com
The evolutionary emergence of land plant body plans transformed the planet. However, our
understanding of this formative episode is mired in the uncertainty associated with the …

Phylogenetic analysis of SARS-CoV-2 data is difficult

B Morel, P Barbera, L Czech… - Molecular biology …, 2021 - academic.oup.com
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being
published on a daily basis, including a regularly updated phylogeny on nextstrain. org. Here …

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

S Guindon, JF Dufayard, V Lefort… - Systematic …, 2010 - academic.oup.com
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML
versions used a fast algorithm performing nearest neighbor interchanges to improve a …

A rapid bootstrap algorithm for the RAxML web servers

A Stamatakis, P Hoover, J Rougemont - Systematic biology, 2008 - academic.oup.com
Despite recent advances achieved by application of high-performance computing methods
and novel algorithmic techniques to maximum likelihood (ML)-based inference programs …

An improved general amino acid replacement matrix

SQ Le, O Gascuel - Molecular biology and evolution, 2008 - academic.oup.com
Amino acid replacement matrices are an essential basis of protein phylogenetics. They are
used to compute substitution probabilities along phylogeny branches and thus the likelihood …

An approximately unbiased test of phylogenetic tree selection

H Shimodaira - Systematic biology, 2002 - academic.oup.com
An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap
technique was developed for general hypothesis testing of regions in an attempt to reduce …

[图书][B] Mathematical population genetics: theoretical introduction

WJ Ewens - 2004 - Springer
Population genetics occupies a central role in a number of important biological and social
undertakings. It is fundamental to our understanding of evolutionary processes, of plant and …

Resolution of the early placental mammal radiation using Bayesian phylogenetics

WJ Murphy, E Eizirik, SJ O'Brien, O Madsen, M Scally… - Science, 2001 - science.org
Molecular phylogenetic studies have resolved placental mammals into four major groups,
but have not established the full hierarchy of interordinal relationships, including the position …