A data-driven framework that profiles per-site bacterial genome variability and simulates evolution from it. From a single genome assembly, SILOSim builds a map of per-site entropy and mobile genetic elements, then runs forward-time simulation weighted by observed variation.
Please be advised that this pipeline is still in its early development stage. It is subject to significant changes in terms of options, outputs, and other functionalities. Users should be prepared for potential modifications and updates in future releases.
Qianxuan (Sean) She
Developed under the mentorship of:
Dr. Paul J. Planet
Email: planetp@chop.edu
Dr. Ahmed M. Moustafa
Email: moustafaam@chop.edu
Dr. Joseph P. Zackular
Email: joseph.zackular@pennmedicine.upenn.edu
