likelihood.msa: MSA Likelihood
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Author(s) See Also Examples

Likelihood of an alignment given a tree model

1	likelihood.msa(x, tm, features = NULL, by.column = FALSE)

`x`	An object of class `msa` representing the multiple alignment
`tm`	An object of class `tm` representing the tree and model of substitution
`features`	A features object. If non-null, compute likelihoods for each feature rather than the whole alignment.
`by.column`	Logical value. If `TRUE`, return the log likelihood for each alignment column rather than total log likelihood. Ignored if features is not NULL.

Either the log likelihood of the entire alignment (if by.column==FALSE && is.null(features), or a numeric vector giving the log likelihood of each feature (if !is.null(features)), or a numeric vector giving the log likelihood of each column (if by.column==TRUE).

Melissa J. Hubisz and Adam Siepel

phyloFit, tm

files <- c("rev.mod", "ENr334-100k.maf", "ENr334-100k.fa", "small.gff")
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
unzip(exampleArchive, files)
msa <- read.msa("ENr334-100k.fa")
mod <- read.tm("rev.mod")
likelihood.msa(msa, mod)
like1 <- likelihood.msa(msa, mod, by.column=TRUE)
length(like1)==ncol.msa(msa)
sum(like1)
msa <- read.msa("ENr334-100k.maf")
likelihood.msa(msa, mod)
like2 <- likelihood.msa(msa, mod, by.column=TRUE)
sum(like2)
mod$subst.mod <- "JC69"
likelihood.msa(msa, mod)
#'
# can also get likelihood by feature
features <- read.feat("small.gff")
features$seqname <- names(msa)[1]
likelihood.msa(msa, mod, features=features)
unlink(files)