cmbuild | R Documentation |
Calls the standalone program cmbuild
from the
Infernal package, which must be
installed. For more information about options, see the
Infernal documentation.
cmbuild( msafile, cmfile_out, name = NULL, force = FALSE, summary_file = NULL, reannotated_msa = NULL, consensus_method = NULL, symfrac = NULL, rsearch = NULL, null = NULL, prior = NULL, weights = NULL, wid = NULL, eff_num = NULL, ere = NULL, eminseq = NULL, emaxseq = NULL, ehmmre = NULL, eset = NULL, p7ere = NULL, p7ml = FALSE, refine = NULL, local = FALSE, gibbs = FALSE, seed = NULL, cyk = FALSE, notrunc = FALSE, extra = NULL, quiet = TRUE )
msafile |
( |
cmfile_out |
( |
name |
( |
force |
( |
summary_file |
( |
reannotated_msa |
( |
consensus_method |
(one of |
symfrac |
( |
rsearch |
( |
null |
( |
prior |
( |
weights |
( |
wid |
( |
eff_num |
( |
ere |
( |
eminseq |
( |
emaxseq |
( |
ehmmre |
( |
eset |
( |
p7ere |
( |
p7ml |
( |
refine |
( |
local |
( |
gibbs |
( |
seed |
( |
cyk |
( |
notrunc |
( |
extra |
( |
quiet |
( |
NULL
, invisibly
cmbuild( msafile = stk_5_8S(), cmfile_out = "/dev/null", force = TRUE, quiet = FALSE )
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