apex (version 1.0.6)

multidna2alignment: Convert from multidna into alignment (seqinr)

Description

The functions multidna2alignment and multiphyDat2alignment concatenates separate sequences and return an alignment object of the seqinr package.

Usage

multidna2alignment(x, genes = TRUE)
multiphyDat2alignment(x, genes = TRUE)

Value

a alignment object

Arguments

x

a multidna or multiphyDat object.

genes

an optional vector indicating the genes to retain for the concatenation; any way to subset the list in x@dna or x@seq is acceptable; by default, all genes are used.

Author

Thibaut Jombart , Zhian N. Kamvar, Klaus Schliep

See Also

• concatenate

• as.alignment to convert single DNAbin objects.

Examples

## simple conversion with nicely ordered output
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
x
y <- multidna2alignment(x)
y
x2 <- multidna2multiphyDat(x)
z <- multiphyDat2alignment(x2)