Table 1 FreeContact command-line parameters

--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]