In this file, I provided Python scripts for working with biological sequences and phylogenetic trees. This tutorial assumes you are familiar with basic bioinformatic tasks and their extension to computational evolutionary models.
For this tutorial, you should already have Python 3.9 or higher, jupyter notebook along with the following libraries:
numpy, ete3, biopython, seaborn, matplotlib and pandas
To install the package you can simply download the repository and run the following command in the root directory.
Install the dependencies using this command:
pip3 install -r requirements.txtShows how to load sequence data and perform simple data structure tasks.
Shows how to load phylogenetic tree and perform simple data structure tasks.
Visualizing posterior probability profile, indel points and etc.
Measuring the dynamic of gaps and indels.
Converting existing exchangalbility matrices to generator 'Q' matrix for WAG and LG models.
If you want to contribute to this repo, submit a pull request!
Gholam-Hossein Jowkar