guidance: MSA Reliability Assessment with GUIDANCE
In heibl/polenta: Multiple Sequence Alignment with PASTA and GUIDANCE

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 `DNAbin` or `AAbin` containing unaligned sequences of DNA or amino acids.
`bootstrap`	An integer giving the number of alternative MSAs to be computed.
`method`	A character string containing further arguments passed to MAFFT; default is `"auto"`.
`msa.exec`	A character string giving the path to the executable of the alignment program (e.g. `/usr/local/bin/mafft`); possible programs are `MAFFT`, `MUSCLE`, `ClustalO`, and `ClustalW`.
`ncore`	An integer specifying the number of cores; default = 1 (i.e. serial execution); `"auto"` can be used for automated usage of all detected cores.
`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

## 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)