molepi-tools

Links to code for inferring who infected whom

• Max Lau's (@msylau) approach, C++
  • Paper
  • Code
• SCOTTI, BEAST2 package
  • Paper
  • Code
• bitrugs, R package
  • Paper
  • Code
• BEASTLIER, BEAST1 hacking/BEAST2 package
  • Paper
  • Code
• TransPhyloMatlab, Matlab (can work in Octave)
  • Paper
  • Code
• TransPhylo, R package
  • Paper
  • Code
• SeqTrack, in R package adegenet
  • Paper
  • Code
• Outbreaker, R package
  • Paper
  • Code
• Outbreaker2, R package
  • Code
• o2mod.transphylo: TransPhylo model as an Outbreaker2 module
  • Code
• Eben Kenah's approach (R code in supplement)
  • Paper
• phybreak, R package
  • Paper
  • Code
• phylo.source.attribution (in phydynR package)
  • Paper
  • Code
• genPOMP (C++)
  • Paper
  • Code
• transcluster (R)
  • Paper
  • Code
• TTsampler, R package
  • Paper
  • Code
• Corander lab ABC approach (Matlab)
  • Paper
  • Code (as supplementary information)
• TransPairs (Matlab)
  • Paper
  • Code
• BADTRIP, BEAST2 package
  • Paper
  • Code
• QUENTIN
  • Paper
  • Matlab version
  • Python version
• Phyloscanner (Python/R)
  • Paper
  • Code

Other relevant papers

There are also some papers describing algorithms for which code is apparently lacking or available only on request:

• Cottam et al. (2008)
  • Paper
• Allen and Velsko (2009)
  • Paper
• Aldrin et al. (2011)
  • Paper
• Ypma et al. (2011)
  • Paper
• Morelli et al. (2012)
  • Paper
• Ypma et al. (2013)
  • Paper
• Mollentze et al. (2014)
  • Paper
• Numminen et al. (2014)
  • Paper
• Velsko et al. (2014)
  • Paper
• Worby et al. (2017)
  • Paper
• Campo et al. (2016), MinDist
  • Paper
• Glebova et al. (2017), MinDistB and ReD
  • Paper
• Tsyvina et al. (2017)
  • Paper
• Rytsareva et al. (2017)
  • Paper