Plotting membrane protein families, highlighting the membrane topology and other evolutionary information using iTOL

Note that Python scripts are required to be run with Python 3.6+.

Nanjiang Shu

National Bioinformatics Infrastructure Sweden

Eamil: nanjiang.shu@scilifelab.se

• FastTree (http://www.microbesonline.org/fasttree/)
• EMBOSS (https://www.ebi.ac.uk/Tools/emboss/)
• CD-HIT (http://weizhongli-lab.org/cd-hit/)

It is highly recommended to use the Python virtual environment to run the pipeline

Set up the virtual environment by running

virtualenv venv

Then activate the environment by

source venv/bin/activate

After that, you can install the Python dependencies by

pip install -r requirements.txt

In the folder test, run

../topoana_TMpro.sh -anamode 2 -outpath out1  -datapath data PF00032

The result will be output to the folder out1