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Table 1 FreeContact command-line parameters

From: FreeContact: fast and free software for protein contact prediction from residue co-evolution

--clustpc BLOSUM-style sequence clustering percentage [0–100]
--cov20 when true, one amino acid is left out when forming the covariance matrix, making it non-overdetermined [10] [Boolean]
--density target precision matrix density [0–1]
--estimate-ivcov perform inverse covariance matrix estimation instead of matrix inversion [Boolean]
--apply-gapth exclude alignment columns with a weighted gap frequency greater than --gapth from the covariance matrix [Boolean]
--gapth weighted gap frequency threshold (0–1]
--icme-timeout inverse covariance matrix estimation timeout in seconds [0-)
--mincontsep minimum sequence separation (j - i ≥ arg) for reporting contacts [1-)
--pseudocnt pseudo-count for sequence weighting [0-)
--pscount-weight pseudo-count weight for sequence weighting [0–1]
--rho initial value of GLASSO regularization parameter [0-)
--parprof parameter profile selection [evfold|psicov|psicov-sd]
  1. FreeContact command-line parameters controlling contact prediction.