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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process

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PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference

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ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

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Computational Molecular Evolution

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ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution

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Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

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ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

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Computing Bayes factors using thermodynamic integration.

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Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

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Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?

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Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens

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Pine Wood Nematode, Bursaphelenchus xylophilus

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Characterization of an indoleamine 2,3-dioxygenase-like protein found in humans and mice

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Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish

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Resolving the evolutionary relationships of molluscs with phylogenomic tools

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INDELible: A Flexible Simulator of Biological Sequence Evolution

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Molecular phylogenetics: state-of-the-art methods for looking into the past

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Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

Waite, D. W., Vanwonterghem, I., Rinke, C., Parks, D. H., Zhang, Y., Takai, K., Sievert, S. M., Simon, J., Campbell, B. J., Hanson, T. E., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00682 · Cited by 408 · see citing works

Accurate and complete genomes from metagenomes

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Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection

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Long-term phosphorus fertilisation increased the diversity of the total bacterial community and the phoD phosphorus mineraliser group in pasture soils

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Coalescent methods for estimating phylogenetic trees

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A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

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Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

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Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer

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Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

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Empirical profile mixture models for phylogenetic reconstruction

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PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation

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Gut microbes of mammalian herbivores facilitate intake of plant toxins

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Endosymbiotic origin and differential loss of eukaryotic genes

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The Fecal Virome of Pigs on a High-Density Farm

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FastML: a web server for probabilistic reconstruction of ancestral sequences

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A Phylogenomic Approach to Resolve the Arthropod Tree of Life

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Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

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A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.

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Genomic data do not support comb jellies as the sister group to all other animals

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Bayesian Analysis of Molecular Evolution Using MrBayes

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Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

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Azadinium spinosumgen. et sp. nov. (Dinophyceae) identified as a primary producer of azaspiracid toxins

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Potyviruses and the Digital Revolution

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Analysis of the Amborella trichopoda Chloroplast Genome Sequence Suggests That Amborella Is Not a Basal Angiosperm

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Identification of olivetolic acid cyclase from <i>Cannabis sativa</i> reveals a unique catalytic route to plant polyketides

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Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa

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Dyneins Across Eukaryotes: A Comparative Genomic Analysis

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The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups

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Molecular Evolution

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ConSurf‐DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins

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Incongruence in the phylogenomics era

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Ecological and evolutionary factors underlying global and local assembly of denitrifier communities

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Improving Amino-Acid Substitution Modelling

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Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method

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Data-specific substitution models improve protein-based phylogenetics

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Phylogenetic mixture models for proteins

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Modelling Protein Evolution

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