Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

(2018) Evelien M. Adriaenssens et al.   ARCHIVES OF VIROLOGY

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy

(2018) Pakorn Aiewsakun et al.   JOURNAL OF GENERAL VIROLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

(2017) Elliot J Lefkowitz et al.   NUCLEIC ACIDS RESEARCH

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

Bacteriophage evolution differs by host, lifestyle and genome

(2017) Travis N. Mavrich et al.   Nature Microbiology

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Linking Virus Genomes with Host Taxonomy

(2016) Tomoko Mihara et al.   Viruses-Basel

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

Methods for virus classification and the challenge of incorporating metagenomic sequence data

(2015) P. Simmonds   JOURNAL OF GENERAL VIROLOGY

Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

(2014) Evelien M. Adriaenssens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth

(2014) Daniel J. G. Lahr et al.   BIOESSAYS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Concatenated alignments and the case of the disappearing tree

(2014) Thorsten Thiergart et al.   BMC EVOLUTIONARY BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae

(2014) Julianne H. Grose et al.   VIROLOGY

The distribution and impact of viral lineages in domains of life

(2014) Arshan Nasir et al.   Frontiers in Microbiology

Characterization of Bacteriophages Cp1 and Cp2, the Strain-Typing Agents for Xanthomonas axonopodis pv. citri

(2013) Abdelmonim Ali Ahmad et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of Novel Virulent Broad-Host-Range Phages of Xylella fastidiosa and Xanthomonas

(2013) S. J. Ahern et al.   JOURNAL OF BACTERIOLOGY

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

(2013) Jenna Morgan Lang et al.   PLoS One

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

(2012) John J. Wiens et al.   PLoS One

Using Supermatrices for Phylogenetic Inquiry: An Example Using the Sedges

(2012) Cody E. Hinchliff et al.   SYSTEMATIC BIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Mosaic Graphs and Comparative Genomics in Phage Communities

(2010) Mahdi Belcaid et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Diversity of Prophages in Dominant Staphylococcus aureus Clonal Lineages

(2009) C. Goerke et al.   JOURNAL OF BACTERIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach

(2009) Sean D. Hooper et al.   NUCLEIC ACIDS RESEARCH

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

(2009) Robert C. Thomson et al.   SYSTEMATIC BIOLOGY

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Bacteriophage genomics

(2008) Graham F Hatfull   CURRENT OPINION IN MICROBIOLOGY

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION