guidanceSA: Interface to guidance program

In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

Description

Interface to guidance program

Usage

guidanceSA(sequences, bootstrap, msa.program, program, gencode, outorder,
  msafile, cutoff = 0.93, moreArgs, exec, proc_num, quiet = FALSE)

Arguments

sequences	An object of class DNAbin or AAbin containing unaligned sequences of DNA or amino acids.
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.

Value

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

Author(s)

Franz-Sebastian Krah

heibl/polenta documentation built on May 17, 2019, 3:22 p.m.