CTree: comparison of clusters between phylogenetic trees made easy. - John P. Archer; David L. Robertson (Bioinform., 2007)

Identifying the Important HIV-1 Recombination Breakpoints. - John P. Archer; John W. Pinney; Jun Fan; Etienne Simon-Loriere; Eric J. Arts; Matteo Negroni; David L. Robertson (PLoS Comput. Biol., 2008)

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time - An Ultra-Deep Approach. - John P. Archer; Andrew Rambaut; Bruce E. Taillon; P. Richard Harrigan; Marilyn Lewis; David L. Robertson (PLoS Comput. Biol., 2010)

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. - John P. Archer; Greg Baillie; Simon J. Watson 002; Paul Kellam; Andrew Rambaut; David L. Robertson (BMC Bioinform., 2012)

VTBuilder: a tool for the assembly of multi isoform transcriptomes. - John P. Archer; Gareth Whiteley; Nicholas R. Casewell; Robert A. Harrison; Simon C. Wagstaff (BMC Bioinform., 2014)

CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure. - Raquel Linheiro; John P. Archer (PLoS Comput. Biol., 2021)