DeepMSA

git clone https://github.com/kad-ecoli/MSAParser.git

Or simply get the related file for NEFF calculation from https://github.com/kad-ecoli/MSAParser/blob/master/calNf.cpp

For getting the executable: g++ -O3 calNf.cpp -o calNf

Gremlin

git clone https://github.com/sokrypton/GREMLIN_CPP.git

Or simply get https://github.com/sokrypton/GREMLIN_CPP/blob/master/gremlin_cpp.cpp

For getting the executable: g++ -O3 gremlin_cpp.cpp -o gremlin_cpp -fopenmp

rMSA

git clone https://github.com/pylelab/rMSA.git

Or simply get https://github.com/pylelab/rMSA/blob/master/src/fastNf.cpp

For getting the executable: g++ -O3 fastNf.cpp -o fastNf

Conkit

pip install conkit

RaptorX

Use RaptorX-3DModeling/BuildFeatures/Helpers/CalcMeff.py