Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Defining the Phylogenomics of Shigella Species: a Pathway to Diagnostics

(2015) Jason W. Sahl et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes

(2015) Olivier Clermont et al.   MICROBIOLOGY-SGM

Phylogenomic evaluation of members above the species level within the phylumFirmicutesbased on conserved proteins

(2015) Weiwei Zhang et al.   Environmental Microbiology Reports

Fast alignment-free sequence comparison using spaced-word frequencies

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

(2014) Sebastian Horwege et al.   NUCLEIC ACIDS RESEARCH

Recombination Blurs Phylogenetic Groups Routine Assignment in Escherichia coli: Setting the Record Straight

(2014) María-Carmen Turrientes et al.   PLoS One

Molecular phylogenetics before sequences

(2014) Mark A Ragan et al.   RNA Biology

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Inferring phylogenies of evolving sequences without multiple sequence alignment

(2014) Cheong Xin Chan et al.   Scientific Reports

Antibacterial gene transfer across the tree of life

(2014) Jason A Metcalf et al.   eLife

The PVC superphylum: exceptions to the bacterial definition?

(2013) John A. Fuerst   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Alignment-free phylogenetics and population genetics

(2013) B. Haubold   BRIEFINGS IN BIOINFORMATICS

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

(2013) O. Bonham-Carter et al.   BRIEFINGS IN BIOINFORMATICS

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

(2013) K. Song et al.   BRIEFINGS IN BIOINFORMATICS

Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria

(2013) K. P. Williams et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A Phylum-Level Bacterial Phylogenetic Marker Database

(2013) Zhang Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis reveals the coexistence of interfamily and interspecies horizontal gene transfer in Streptococcus thermophilus strains isolated from the same yoghurt

(2013) Xuerui Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Co-phylog: an assembly-free phylogenomic approach for closely related organisms

(2013) Huiguang Yi et al.   NUCLEIC ACIDS RESEARCH

Alignment-free phylogeny of whole genomes using underlying subwords

(2012) Matteo Comin et al.   Algorithms for Molecular Biology

Evolutionary Implications of Horizontal Gene Transfer

(2012) Michael Syvanen   Annual Review of Genetics

Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi

(2012) F. E. Loffler et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

MRSA epidemic linked to a quickly spreading colonization and virulence determinant

(2012) Min Li et al.   NATURE MEDICINE

Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae

(2011) Hiromi Nishida et al.   GENOMICS

Alveolate Phylogeny Inferred using Concatenated Ribosomal Proteins

(2011) TSVETAN R. BACHVAROFF et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T)

(2011) Marcel Huntemann et al.   Standards in Genomic Sciences

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

The Tree and Net Components of Prokaryote Evolution

(2010) Pere Puigbò et al.   Genome Biology and Evolution

Phylogeny of Gammaproteobacteria

(2010) K. P. Williams et al.   JOURNAL OF BACTERIOLOGY

Recent Trends in Molecular Phylogenetic Analysis: Where to Next?

(2010) C. Blair et al.   JOURNAL OF HEREDITY

A phylum level perspective on bacterial cell envelope architecture

(2010) Iain C. Sutcliffe   TRENDS IN MICROBIOLOGY

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

(2009) Carsten Kemena et al.   BIOINFORMATICS

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater

(2009) W. M. Moe et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Estimating Mutation Distances from Unaligned Genomes

(2009) Bernhard Haubold et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

(2009) O. Zhaxybayeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

(2009) Gregory E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

The Impact of Reticulate Evolution on Genome Phylogeny

(2008) Robert G. Beiko et al.   SYSTEMATIC BIOLOGY