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A clean-room reimplementation of Chris Sander / Debora S Marks' EVFold
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README.md

README.md

EVFold Reimplementation

This is a clean-room reimplementation of EVFold ( www.evfold.org )

I am sorry about its state.

Running: (in the bash shell)

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.
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