Please document how to download, install and run this program in your preferred way

[Masterxilo]

We currently use a certain commit/branch:

Currently we effectively do

git clone https://github.com/medvir/SmaltAlign && git checkout 0fa89ceec7ecb0697721e586d814b2a7f6724739

so the state of the repository of https://github.com/medvir/SmaltAlign/tree/0fa89ceec7ecb0697721e586d814b2a7f6724739 from Sep 17, 2021

note: that commit is the head of non-main branch "handle_triplet_SNVs"

It would be good if the best version was properly tagged/released and if the version on the master branch would include the improvements of this branch.

Also, branches that are integrated into master can be deleted so that they don't confuse future users.

You mentioned there is a python package - how would that be used?