Whole Genome Sequencing Allows Better Understanding of the Evolutionary History of Leptospira interrogans Serovar Hardjo

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus

(2013) Joon Tan et al.   BMC GENOMICS

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

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array

(2010) V. L. Arcus et al.   PROTEIN ENGINEERING DESIGN & SELECTION

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Efflux-Mediated Drug Resistance in Bacteria

(2009) Xian-Zhi Li et al.   DRUGS

A century of Leptospira strain typing

(2009) Gustavo M. Cerqueira et al.   INFECTION GENETICS AND EVOLUTION

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Characterizing positive and negative selection and their phylogenetic effects

(2008) Steven E. Massey et al.   GENE