HoT: Heads or Tails Alignment Reliability

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

Heads or Tails Alignment Reliability

Description

MSA reliability assessment HoT (Landan and Graur 2008)

Usage

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

Arguments

sequences	object of class DNAbin or AAbin containing unaligned sequences of DNA or amino acids.
method	further argument passed to MAFFT, default is "auto"
bootstrap	integer giving the number of alternative MSAs to be computed
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	integer specifying the number of cores; default = 1 (serial), "auto" can be used for automated usage of all detected cores.
zip.file	A character string giving the name for the output zip file.

Details

Calculates column reliability (and other scors) by comparing alternative MSAs generated by aligning guide tree partitions as described in Landan and Graur (2008). For details see compareMSAs. 8*(N-3) alternative MSAs are generated by default, where N is the number of sequences.

For an example workflow see Vignette

Value

An object of class guidanceDNA or guidanceAA.

Author(s)

Franz-Sebastian Krah

References

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

See Also

msa_set_score, guidance, guidance2

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

## End(Not run)

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