guidance2: MSA Reliability Assessment with GUIDANCE2

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

MSA Reliability Assessment with GUIDANCE2

Description

Calculate MSA reliability scores with GUIDANCE2 (Sela et al. 2015).

Usage

guidance2(sequences, bootstrap = 100, method = "auto", n.coopt = 4,
  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".
n.coopt	An integer giving the number of sampled co-optimal MSAa.
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, and ClustalW. For details see clustal, mafft
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.

Details

Calculates column confidence (and other scors) by comparing alternative MSAs generated by the GUIDANCE with varying gap opening panelty and the HoT methodology. First 100 alternative MSAs (with BP guide trees) with varying gap opening panelty are produced, then for each n (default = 4) co-optimal alignments are produced using HoT. 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).

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.

Landan and Graur. 2008. Local reliability measures from sets of co-optimal multiple sequence alignments. Pacific Symposium on Biocomputing 13:15–24.

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

Sela et al. 2015. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Research 43:W7–W14

See Also

guidance, 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 <- guidance2(sequences = fas, msa.exec= "/usr/local/bin/mafft")
scores <- scores(g, score = "column")
plot(scores$column$score, xlab = "Site", 
ylab = "Column score", 
main = "GUIDANCE2", type ="l")

## End(Not run)

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