Table 1.

Available software tools for viral quasispecies inference.

Program	Method	URL	References
QuRe	Read graph	http://sourceforge.net/projects/qure/	Prosperi and Salemi, 2012
ShoRAH	Read graph	http://www.cbg.ethz.ch/software/shorah	Zagordi et al., 2011
ViSpA	Read graph	http://alla.cs.gsu.edu/~software/VISPA/vispa.html	Astrovskaya et al., 2011
BIOA	Read graph	https://bitbucket.org/nmancuso/bioa/	Mancuso et al., 2011
Hapler	Read graph	http://nd.edu/~biocmp/hapler/	O'Neil and Emrich, 2012
AmpliconNoise	Probabilistic	http://code.google.com/p/ampliconnoise	Quince et al., 2011
PredictHaplo	Probabilistic	http://www.cs.unibas.ch/personen/roth_volker/HivHaploTyper	Prabhakaran et al., 2010
QuasiRecomb	Probabilistic	http://www.cbg.ethz.ch/software/quasirecomb	Zagordi et al., 2012