GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

(2012) Rolf S Kaas et al.   BMC GENOMICS

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

(2012) Yuri I. Wolf et al.   Genome Biology and Evolution

PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species

(2012) Derrick E. Fouts et al.   NUCLEIC ACIDS RESEARCH

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Gene Repertoire Evolution of Streptococcus pyogenes Inferred from Phylogenomic Analysis with Streptococcus canis and Streptococcus dysgalactiae

(2012) Tristan Lefébure et al.   PLoS One

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

PGAP: pan-genomes analysis pipeline

(2011) Yongbing Zhao et al.   BIOINFORMATICS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information

(2011) T. Schmitt et al.   BRIEFINGS IN BIOINFORMATICS

Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution

(2011) Haruo Suzuki et al.   Genome Biology and Evolution

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

A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches

(2010) David M. Kristensen et al.   BIOINFORMATICS

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

(2010) Chad Laing et al.   BMC BIOINFORMATICS

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Standard operating procedure for computing pangenome trees

(2010) Lars Snipen et al.   Standards in Genomic Sciences

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

(2010) Claudio Donati et al.   GENOME BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Microbial comparative pan-genomics using binomial mixture models

(2009) Lars Snipen et al.   BMC GENOMICS

Screening of Streptococcus pneumoniae ABC Transporter Mutants Demonstrates that LivJHMGF, a Branched-Chain Amino Acid ABC Transporter, Is Necessary for Disease Pathogenesis

(2009) S. Basavanna et al.   INFECTION AND IMMUNITY

Gram-positive toxic shock syndromes

(2009) Emma Lappin et al.   LANCET INFECTIOUS DISEASES

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin et al.   NUCLEIC ACIDS RESEARCH

The National Center for Biotechnology Information's Protein Clusters Database

(2008) William Klimke et al.   NUCLEIC ACIDS RESEARCH