My collection demonstrating useful resources on command line (or in Jupyter environment) for manipulating sequence data.
Select a notebook from this index.
Categorize conservation in a multiple sequence alignment
There is a related notebook available from here for categorizing conservation in a MSA and using that to generate molecular visualization commands that uses categorize_residues_based_on_conservation_relative_consensus_line.py
script described here. It can be launched in active form from here and then selecting from the index to go to the 'Categorize conservation in a MSA and use that to generate molvis commands' page. The demo was put in the structure work demo series because it was mainly developed to work towards making commands for molecular visualization.