Molecular phylogenetics: principles and practice

Z Yang, B Rannala - Nature reviews genetics, 2012‏ - nature.com
Phylogenies are important for addressing various biological questions such as relationships
among species or genes, the origin and spread of viral infection and the demographic …

A biologist's guide to Bayesian phylogenetic analysis

FF Nascimento, M Reis, Z Yang - Nature ecology & evolution, 2017‏ - nature.com
Bayesian methods have become very popular in molecular phylogenetics due to the
availability of user-friendly software for running sophisticated models of evolution. However …

RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language

S Höhna, MJ Landis, TA Heath, B Boussau… - Systematic …, 2016‏ - academic.oup.com
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 …

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

I Sela, H Ashkenazy, K Katoh, T Pupko - Nucleic acids research, 2015‏ - academic.oup.com
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and
comparative genomics studies. However, from the same set of sequences different MSAs …

[کتاب][B] Bayesian evolutionary analysis with BEAST

AJ Drummond, RR Bouckaert - 2015‏ - books.google.com
What are the models used in phylogenetic analysis and what exactly is involved in Bayesian
evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you …

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty

G Baele, P Lemey, T Bedford, A Rambaut… - Molecular biology …, 2012‏ - academic.oup.com
Recent developments in marginal likelihood estimation for model selection in the field of
Bayesian phylogenetics and molecular evolution have emphasized the poor performance of …

Map** the origins and expansion of the Indo-European language family

R Bouckaert, P Lemey, M Dunn, SJ Greenhill… - Science, 2012‏ - science.org
There are two competing hypotheses for the origin of the Indo-European language family.
The conventional view places the homeland in the Pontic steppes about 6000 years ago. An …

Resolving difficult phylogenetic questions: why more sequences are not enough

H Philippe, H Brinkmann, DV Lavrov… - PLoS …, 2011‏ - journals.plos.org
In the quest to reconstruct the Tree of Life, researchers have increasingly turned to
phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box …

BEAST: Bayesian evolutionary analysis by sampling trees

AJ Drummond, A Rambaut - BMC evolutionary biology, 2007‏ - Springer
Background The evolutionary analysis of molecular sequence variation is a statistical
enterprise. This is reflected in the increased use of probabilistic models for phylogenetic …

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

G Talavera, J Castresana - Systematic biology, 2007‏ - academic.oup.com
Alignment quality may have as much impact on phylogenetic reconstruction as the
phylogenetic methods used. Not only the alignment algorithm, but also the method used to …