The '**Results**' directory contains the data that were produced in the study. These data can be produced by the code in th '**Code**' directory and are needed for the production of the figures. This directory does NOT contain all the data produced by the code - however, the intermediate data can be produced by the the code in the '**Code**' directory.
 
  - **Figures** 
  - **HotSpot**
  - **Mixture**

The **Figures** directory contains the figures not produced by the code but needed for creation of complete figure pannels. Also, after running the code present in the **Code/Figures** directory, the figures are saved here.

The **HotSpot** directory contain saple-specific directories concerning the hotspot analysis present in the study. The data produced during the analysis of the HIV-1 intra-Alu integration hotspot are stored in the directories starting with **HIV_** followed by the name of the study (first author).
 
The **Mixtures** directory contains data produced by the EM algorithm. The '**Figures**' folder contains only the figures that cannot be reproduced by any of the code present in the '**Code**' directory. The data in the 'Results' folder should be sufficient to reproduce the Figures present in the publication.

