README.md

SyntenyLink 🧬

Table of Contents 📚

1. Overview
2. Requirements
3. Installation
4. Usage
5. Main programs
6. Contact
7. License

Overview 📖

===========

The SyntenyLink package has six major components: the SyntenyLink algorithm allows users to handle reconstruct subgenomes of polyploid species more conveniently and to separate the set of genes belong to each subgenome in the organism with the aid of reference proteomes of polyploid species and related ancestor. 🌱

All programs are executed using command line options on Linux systems or Mac OS. Usage or help information are well built into the programs. 💻

All code is copiable, distributable, modifiable, and usable without any restrictions.

Requirements 🛠️

=============

To use SyntenyLink, ensure you have the following requirements:

• Python 3.9
• biopython==1.80
• ipython==8.3.0
• matplotlib==3.5.2
• numpy==1.21.5
• pandas==1.4.2
• seaborn==0.11.2
• pickle
• csv
• os
• math
• sys
• re
• warnings
• wandb

Installation ⚙️

=============

1. Clone this repository to your local machine:

git clone git@git.cs.usask.ca:qnm481/syntenylink.git
cd SyntenyLink

2. Install the required dependencies:

pip install -r requirements.txt

3. Reproduce all the experiments: