Plotting MSA

Pymsaviz is a great local and offline multiple sequence alignment (MSA) viewer and plotter alternative to the NCBI online MSA viewer. No frills, easy to install and use and is fantastic for creating publication-grade figures.

I will be using this example to visulise the alignment.

Prerequisite

• Python >= 3.9

Installation

pip install pygenomeviz

or

conda install -c conda-forge -c bioconda pymsaviz

Usage

1. Import package

    from pymsaviz import MsaViz
   

2. Assuming you have run a MSA with an output file called msa.out.fa in the same directory

    msa_file = "./msa.out.fa"
   

3. Create the MSA object.

    mv = MsaViz(msa_file, wrap_length=60, show_count=True)
   

4. Plot and Save.

    mv.savefig("./msa_plot.png")
   

You should see an output like this. (excerpt)

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