ITEP: An integrated toolkit for exploration of microbial pan-genomes

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

(2013) Phillip Seitzer et al.   BMC BIOINFORMATICS

Clustering evolving proteins into homologous families

(2013) Cheong Xin Chan 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

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

Coral: an integrated suite of visualizations for comparing clusterings

(2012) Darya Filippova et al.   BMC BIOINFORMATICS

Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways

(2012) Anthony R Borneman et al.   BMC GENOMICS

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling et al.   BRIEFINGS IN BIOINFORMATICS

Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates

(2012) Sean Conlan et al.   GENOME BIOLOGY

PGAP: pan-genomes analysis pipeline

(2011) Yongbing Zhao et al.   BIOINFORMATICS

OrthoInspector: comprehensive orthology analysis and visual exploration

(2011) Benjamin Linard et al.   BMC BIOINFORMATICS

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

(2011) Caroline B Milne et al.   BMC Systems Biology

Computational methods for Gene Orthology inference

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

PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species

(2011) Joseph J. Gillespie et al.   INFECTION AND IMMUNITY

The Salmonella enterica Pan-genome

(2011) Annika Jacobsen et al.   MICROBIAL ECOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp. bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production

(2011) Pei Hao et al.   PLoS One

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC 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

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Genome-Wide Comparative Gene Family Classification

(2010) Christian Frech et al.   PLoS One

Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses

(2010) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Biogeography of the Sulfolobus islandicus pan-genome

(2009) M. L. Reno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

(2008) Joungmin Lee et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome-scale model forClostridium acetobutylicum: Part I. Metabolic network resolution and analysis

(2008) Ryan S. Senger et al.   BIOTECHNOLOGY AND BIOENGINEERING

JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

(2008) Michael Richter et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS