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Welcome to the DyNoPy tutorial!

Hopefully, you will find the instructions provided here useful on how to use this code.

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General tips

You can invoke the help by using the -h flag. eg:

dyno_coevolution.py -h

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Generating coevolution matrix

dyno_coevolution.py calls the hhblits, hhfilter, egrep to generate the sequence alignment (.aln file) from the Uniref database and ccmpred to generate the coevolution matrix (.mat file) from the alignment.

Options: -i <fasta file>

-n <number of threads to use. For CCMpred GPU is best. Code will check if GPU hardware is available and will decide to use either CPU or GPU for CCMpred

-d <Uniprot/Swiss prot protein sequence database label

Sample usage:

dyno_coevolution.py -i 1btl.fasta -n 12