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 …

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 …

Model selection may not be a mandatory step for phylogeny reconstruction

S Abadi, D Azouri, T Pupko, I Mayrose - Nature communications, 2019 - nature.com
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental
step in numerous evolutionary studies. Over the years, various criteria for model selection …

A species-level phylogeny of extant snakes with description of a new colubrid subfamily and genus

A Figueroa, AD McKelvy, LL Grismer, CD Bell… - PloS one, 2016 - journals.plos.org
Background With over 3,500 species encompassing a diverse range of morphologies and
ecologies, snakes make up 36% of squamate diversity. Despite several attempts at …

[PDF][PDF] Mutation rates and selection on synonymous mutations in SARS-CoV-2

N De Maio, CR Walker, Y Turakhia… - Genome biology and …, 2021 - academic.oup.com
The COVID-19 pandemic has seen an unprecedented response from the sequencing
community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes …

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

S Guindon, O Gascuel - Systematic biology, 2003 - academic.oup.com
The increase in the number of large data sets and the complexity of current probabilistic
sequence evolution models necessitates fast and reliable phylogeny reconstruction …

Initial sequencing and comparative analysis of the mouse genome

European Bioinformatics Institute: Birney Ewan 3 … - Nature, 2002 - nature.com
The sequence of the mouse genome is a key informational tool for understanding the
contents of the human genome and a key experimental tool for biomedical research. Here …

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 …

[图书][B] Evolution: Probleme—Themen—Fragen

M Ridley - 2013 - books.google.com
Beim Studium der jüngeren Kontroversen über den Darwinismus fiel mir wiederholt auf, das
sie falsche Darstellungen enthielten, so als würde es sich um irgendetwas Umfassenderes …

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 …