guidance: MSA Reliability Assessment with GUIDANCE

In FranzKrah/rGUIDANCE: rGUIDANCE – alignment confidence score computation in R

MSA Reliability Assessment with GUIDANCE

Description

Calculate MSA reliability scores with GUIDANCE (Penn et al. 2010).

Usage

guidance(sequences, bootstrap = 100, method = "auto",
  msa.exec = "/usr/local/bin/mafft", ncore = 1, zip.file)

Arguments

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, ClustalW, ClustalO or PRANK For details see clustal, mafft, prank
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 dir of zip-compressed file to be produced, which contains the alternative MSAs. If left empty (default), the alternative MSA will not be stored and cannot be assessed by the user.

Details

Calculates column confidence (and other scores) by comparing alternative MSAs generated by alternative guide trees derived from bootstrapped MSAs (Felsenstein 1985). The basic comparison between the bootstrapped MSAs and a reference MSA is if column residue pairs are identically aligned in all alternative MSAs compared with the base MSA (see msa_set_score).

For an example workflow see Vignette

Value

An object of class guidanceDNA or guidanceAA.

Author(s)

Franz-Sebastian Krah

References

Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791.

Penn et al. 2010. An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27:1759–1767.

See Also

msa_set_score, guidance2, HoT

Examples

## Not run: 
# run GUIDANCE on example data using MAFFT
fpath <- system.file("extdata", "BB30015.fasta", package="rGUIDANCE") # random example from BALiBASE
fas <- ape::read.FASTA(fpath)
g <- guidance(sequences = fas, msa.exec= "/usr/local/bin/mafft")
scores <- scores(g, score = "column")
plot(scores$column$score, xlab = "Site", 
ylab = "Column score", 
main = "GUIDANCE", type = "l")

## End(Not run)

FranzKrah/rGUIDANCE documentation built on Jan. 27, 2024, 10:42 a.m.