Hi everyone,

First of all I have little background in biology but currently doing something in bioinformatics as I am a computer engineering student.

Currently I am trying to recreate the methods done in the paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165451/

I am able to somewhat reproduce everything except for one particular thing: The 11-gene-sliding-window mechanism that they introduced.

The paper only publishes data and not intermediary calculations. Even if the paper describes its method, I find that the 11-gene-sliding-window contradicts to the results they publish.

Questions:

1. Has anyone ever tried attempting to reverse engineer the sliding-window and find out?
2. Not related to the methods anyone knows about a database/samples with annotated horizontally transferred genes?