readme.md

uGene

Project snapshot:

With uGene, phylogenetic profiles can be read and clustered with uMap. Groups of genes or taxa of particular interest can be exported.

Installation:

Direct Download:

• Download from: https://github.com/BIONF/uGene/
• Extract to your desired location.

Via Pip:

1. Open 'packages.txt'.
2. Run: pip install -r requirements.txt

Via Conda/Pip:

1. Install Anaconda.
2. Execute: conda create -n uGene conda activate uGene conda install pip pip install -r requirements.txt

Enable PhyloProfile Support:

1. Install PhyloProfile. Visit: https://github.com/BIONF/PhyloProfile for install instructions.
2. Use PhyloProfile to open and parse your taxa. Ensuring all taxa are recognized.
3. Ensure R is installed and on your system's PATH.

Start uGene:

You can use uGene via command-line or the dashboard.

Command-line use:

python uGeneCore.py -h

Garfic-Interface use:

python uGeneGUI.py

Usage:

Within the "example" directory in the file location, you'll find two sets of data samples. The first set showcases simulated data, while the second features genuine data. Open the .phyloprofile or the respective .cluster.csv files. Use the graphical interface of uGenGUI to do so.