Tutorial

Dataset

Here is a full dataset description: Analysis of genetic and climatic data of SARS-CoV-2

Koshkarov, A., Li, W., Luu, M. L., & Tahiri, N. (2022). Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2.

Step by step

Running the application

1. Clone the repository

git clone https://github.com/tahiri-lab/iPhyloGeo_plus_plus.git
cd iPhyloGeo_plus_plus

2. Set Up a Virtual Environment

python3 -m venv iPhyloGeo++_env   # Use only `python` instead of `python3` if it doesn't work

# Linux
source iPhyloGeo++_env/bin/activate  

# Windows 
iPhyloGeo++_env\Scripts\activate

3. Install Dependencies

pip install -r requirements.txt

4. Run the Application

cd scripts
python3 main.py

Run your first genetic analysis

genetic_tuto.mp4

The sequence alignment can be modified by changing its settings. Once the alignment is done, you will see a representation of the differences between each DNA from the FASTA file.

From this point you will be able to plot the species statistics and the genetic tree that will be used for the results, coupled with the climatic tree.

The result of the genetic part is a dynamic diagram that shows the similarities between each species in the FASTA file. In the left column you can find the name of each species. In the right, you can find a table showing the molecule comparison of each species' DNA. In this table you can change the starting position and the window size.

The statistics diagram follows the same principle. You can see the DNA difference between each species but with a statistic method where you can select which DNA reference to compare the other species with.

Run your first climatic analysis

climatic_tutorial.mp4

The uploaded file needs to be a .CSV file and can contain geographic locations data as latitude and longitude values. There is no download limitations for the graphs and trees representations. The graphs and trees downloaded are exported in .PNG as default but the extension can be changed at the user's will.

Get your results and export them

results_tutorial.mp4

The Results section is only available once a file has been uploaded in the Climatic session, and once a sequence alignment has been done in the Genetic section.

The Settings are not mandatory but the user can modify them to adapt the generation to its needs. More information about the settings are provided in the User Preferences section in the Wiki.

Every files generated by the user is exported in the results folder, found in the scripts folder. It includes every trees and similarity representation and the final table exported as output.csv