This version of Zephyr should be cited as:

Maddison, D.R., & W.P. Maddison. 2017. Zephyr: a Mesquite package for interacting with external phylogeny inference programs. Version 2.01. https://mesquitezephyr.wikispaces.com

You should also cite the external programs that you used in conjunction with Zephyr, such as GARLI, RAxML, PAUP, TNT, etc.