my final year at Wesleyan I worked on a bacterial sepciation software simulation program called Ecotype Simulation (ES). My thesis was a write up on new improvements made to the algorithm and a comparison to other speciation simulation algorithms. Eventually I plan to write up more clearly what the algorithm actually did but for now I’ll just leave the link to my thesis. Where I should do a pretty thorough job of doing just that. Who knows. Still if you are interested in bacterial speciation then it might be worth a read.
The first and second
chapters are good introductions to the problem we were analyzing. After that we have a section on improvements and testing those improvements before a mini-conclusion. I struggled to understand parts of ES when I just started at the Cohan lab. Which is why I intended to write as simple a description of how the algorithm works as possible. Anyways, here we have the WesScholar profile, and the thesis link.