Description Usage Arguments Details Value Author(s) References See Also Examples
Calculate MSA reliability scores with GUIDANCE (Penn et al. 2010).
1 2 | guidance(sequences, bootstrap = 100, method = "auto",
msa.exec = "/usr/local/bin/mafft", ncore = 1, zip.file)
|
sequences |
An object of class |
bootstrap |
An integer giving the number of alternative MSAs to be computed. |
method |
A character string containing further arguments passed to
MAFFT; default is |
msa.exec |
A character string giving the path to the executable of the
alignment program (e.g. |
ncore |
An integer specifying the number of cores; default = 1 (i.e.
serial execution); |
zip.file |
A character string giving the name of zip-compressed file, which contains the alternative MSAs. If left empty (default), the alternative MSA will not be stored and cannot be assessed by the user. |
Calculates column confidence (and other scors) by comparing
alternative MSAs generated by alternative guide trees derived from
bootstrap MSAs (Felsenstein 1985). The basic comparison between the BP MSAs
and a reference MSA is if column residue pairs are identically aligned in
all alternative MSAs compared with the base MSA (see compareMSAs
).
An object of class polentaDNA
or
polentaAA
.
Franz-Sebastian Krah
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783<e2><80><93>791.
Landan, G. and Graur, D. 2008. Local reliability measures from sets of co-optimal multiple sequence alignments. Pacific Symposium on Biocomputing 13:15–24.
Penn, O., Privman, E., Landan, G., Graur, D. and Pupko, T. 2010. An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27:1759–1767.
msa_set_scoreR
, guidance2
,
HoT
1 2 3 4 5 6 7 8 9 | ## Not run:
# run GUIDANCE on example data using MAFFT
file <- system.file("extdata", "BB50009.fasta", package = "polenta")
aa_seq <- read.fas(file)
g_res <- guidance(sequences = aa_seq)
scores <- daughter_scores(g_res, score = c("gcsc", "rprsc"))
hist(scores$gcsc$score, xlab = "Column score", main = "GUIDANCE")
## End(Not run)
|
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