Prokaryotic taxonomy and nomenclature in the age of big sequence data
The classification of life forms into a hierarchical system (taxonomy) and the application of
names to this hierarchy (nomenclature) is at a turning point in microbiology. The …
names to this hierarchy (nomenclature) is at a turning point in microbiology. The …
A RESTful API for access to phylogenetic tools via the CIPRES science gateway
The CIPRES Science Gateway is a community web application that provides public access
to a set of parallel tree inference and multiple sequence alignment codes run on large …
to a set of parallel tree inference and multiple sequence alignment codes run on large …
Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to
modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of …
modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of …
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
Background The extant squamates (> 9400 known species of lizards and snakes) are one of
the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have …
the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have …
A species-level phylogeny of extant snakes with description of a new colubrid subfamily and genus
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 …
ecologies, snakes make up 36% of squamate diversity. Despite several attempts at …
A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians
The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>
6800 species). Despite much recent focus on their conservation, diversification, and …
6800 species). Despite much recent focus on their conservation, diversification, and …
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
Previous analyses of relations, divergence times, and diversification patterns among extant
mammalian families have relied on supertree methods and local molecular clocks. We …
mammalian families have relied on supertree methods and local molecular clocks. We …
Molecular phylogenetics: principles and practice
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 …
among species or genes, the origin and spread of viral infection and the demographic …
Comparative genomics of biotechnologically important yeasts
Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here,
we report the comparative genome analysis of 29 taxonomically and biotechnologically …
we report the comparative genome analysis of 29 taxonomically and biotechnologically …
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
M Schubert, L Ermini, CD Sarkissian, H Jónsson… - Nature protocols, 2014 - nature.com
Next-generation sequencing technologies have revolutionized the field of paleogenomics,
allowing the reconstruction of complete ancient genomes and their comparison with modern …
allowing the reconstruction of complete ancient genomes and their comparison with modern …