Acknowledgments and citations

Acknowledgments

phydms is written by the Bloom lab (see the full list of contributors).

Citations

The current citation for phydms is Hilton, Doud, and Bloom, PeerJ, 2017. Please cite this paper if you use phydms!

The following references are also relevant to the ExpCM implemented by phydms:

• Bloom, Biology Direct, 12:1

• Bloom, Mol Biol Evol, 31:1956-1978

• Bloom, Mol Biol Evol, 31:2753-2769

If you use any of the simulation capabilities of phydms, please also cite pyvolve:

• Spielman and Wilke, PLoS One, 10:e0139047

If you use phydms_logoplot to create logo plots, please also cite weblogo:

• Crooks et al, Genome Research, 14:1188-1190

Finally, if you use dms_tools2 to process your deep mutational scanning data before feeding it into phydms, please cite:

• Bloom, BMC Bioinformatics, 16:168