Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

Enzyme Recruitment and Its Role in Metabolic Expansion

(2014) Cindy Schulenburg et al.   BIOCHEMISTRY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

A systematic comparison of the MetaCyc and KEGG pathway databases

(2013) Tomer Altman et al.   BMC BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

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

(2013) Nicola Segata et al.   Nature Communications

Computational tools for metabolic engineering

(2012) Wilbert B. Copeland et al.   METABOLIC ENGINEERING

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

A survey of metabolic databases emphasizing the MetaCyc family

(2011) Peter D. Karp et al.   ARCHIVES OF TOXICOLOGY

Consistency of gene starts among Burkholderia genomes

(2011) John Dunbar et al.   BMC GENOMICS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Genome Majority Vote Improves Gene Predictions

(2011) Michael E. Wall et al.   PLoS Computational Biology

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Horizontal gene transfer in evolution: facts and challenges

(2009) L. Boto   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

The prokaryotic tree of life: past, present…and future?

(2008) James O. McInerney et al.   TRENDS IN ECOLOGY & EVOLUTION