Using the taxon-specific genes for the taxonomic classification of bacterial genomes

Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades

(2014) Radhey S. Gupta et al.   ANAEROBE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Molecular signatures for members of the genus Dehalococcoides and the class Dehalococcoidia

(2014) D. A. Ravinesan et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives

(2014) Mohammad Howard-Azzeh et al.   PHOTOSYNTHESIS RESEARCH

Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species

(2014) Amandeep Sawana et al.   Frontiers in Genetics

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Defining bacterial species in the genomic era: insights from the genus Acinetobacter

(2012) Jacqueline Z-M Chan et al.   BMC MICROBIOLOGY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

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

Notes on the characterization of prokaryote strains for taxonomic purposes

(2009) B. J. Tindall et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A simple method for phylogenomic inference using the information of gene content of genomes

(2008) Hongmei Zhang et al.   GENE

Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium)

(2008) M. Martens et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY