Description Usage Arguments Value Author(s)
Interface to guidance program
1 2 | guidanceSA(sequences, bootstrap, msa.program, program, gencode, outorder,
msafile, cutoff = 0.93, moreArgs, exec, proc_num, quiet = FALSE)
|
sequences |
An object of class |
bootstrap |
An integer giving the number of perturbated MSAs. |
msa.program |
A charcter string giving the name of the MSA program, currelty one of c("mafft", "muscle", "clustalo", "clustalw2"); MAFFT is default |
program |
A charcter string giving the name one of c("guidance", "guidance2", "HoT"). |
gencode |
XXX. |
outorder |
XXX. |
msafile |
XXX. |
cutoff |
XXX. |
moreArgs |
XXX. |
exec |
path to guidance program folder, e.g. "/Applications/guidance.v2.02/" |
proc_num |
Integer giving the number of cores. |
quiet |
logical if TRUE, progress is printed to console. |
list containing following scores and alignments:
mean_scores residue pair score and mean column score
column_score
residue_column_score GUIDANCE score
residue_pair_residue_score
residual_pair_sequence_pair_score
residual_pair_sequence_score
residue_pair_score
base_msa
guidance_msa is the base_MSA removed from unreliable residues/columns/sequences below cutoffs
Franz-Sebastian Krah
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