You need Python to run the scripts. They are old and may only work on py2.7 . (sorry again)

You need the CNS package to do the computation. Licensing prevents me from providing it to you. [ https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/cns/cns_1.3/installation/frame.html ]
There are scripts for CNS version 1.3 and 1.21 . I hope they both work.
Again, I would have liked to provide a docker image for this, but licensing prevents my redistributing CNS. :/

1) Environment
	export PYTHONPATH=./utils/pymodules:${PYTHONPATH}

2) Weighted (.sim) input file.
	./utils/SimpleHammWeight.py <input>.faa <output>.sim

	Be careful, on huge alignments this may take quite a lot of time and memory.
	Consider using hhblits to create your alignments and hhfilt to filter to get fewer sequences with more independence. That will speed things up a lot.
	My favorite settings for hhblits are " -n 4 -nodiff -cov 75 -id 99 -nodiff -neffmax 20 --maxfilt 100000 "
	My favorite settings for hhfilt are " hhfilter -cov 75 -id 95 -i <INTPUT> -o <OUTPUT>"

3)
	consider seeing bin/prepare.bash and Makefile to see how to run the program.