Supported Applications
plmc
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Description
infers undirected graphical models to describe coevolution and covariation in families of biological sequences. With a multiple sequence alignment as an input, plmc can quantify inferred coupling strengths between all pairs of positions (couplingsfile output) or infer a generative model of the sequences for predicting the effects of mutations or designing new sequences (paramfile output).
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Installation
Use the following command to install this title with the CLI client:$ sbgrid-cli install plmc
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Primary Citation*
T. A. Hopf, J. B. Ingraham, F. J. Poelwijk, C. P. I. Schärfe, M. Springer, C. Sander, and D. S. Marks. 2017. Mutation effects predicted from sequence co-variation. Nature Biotechnology. 35: 128-135.
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*Full citation information available through
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Default Versions
Linux 64:  20171002
OS X INTEL:  20171002 -
Developers
Debora S Marks, John Ingraham