I need to use the .chk and .pssm files as input for another program. But I am not very sure how to create .chk files and what they actually are. With 'makemat' I can transform .chk to a matrix, but I could not find out what the numbers in the matrix mean.
It seems that using 'blastpgp' I can create these files if a sequence fasta is given. But I want to work with MSA as input instead. So the other option I looked up is to use 'hmmbuild' to create a PSSM profile from MSA. However, it does not give any .chk file.
So how can I obtain .chk files from a MSA??