PyEvolve: a toolkit for statistical modelling of molecular evolution. - Andrew Butterfield; Vivek Vedagiri; Edward Lang; Cath Lawrence; Matthew J. Wakefield; Alexander Isaev; Gavin A. Huttley (BMC Bioinform., 2004)

Vestige: Maximum likelihood phylogenetic footprinting. - Matthew J. Wakefield; Peter Maxwell; Gavin A. Huttley (BMC Bioinform., 2005)

Xenomapper: Mapping reads in a mixed species context. - Matthew J. Wakefield (J. Open Source Softw., 2016)

SurvivalVolume: interactive volume threshold survival graphs. - Matthew J. Wakefield (J. Open Source Softw., 2016)