aphid (version 1.3.1)

unalign: Deconstruct an alignment.

Description

unalign deconstructs an alignment to a list of sequences.

Usage

unalign(x, gap = "-")

Arguments

x

a matrix of aligned sequences. Accepted modes are "character" and "raw" (for "DNAbin" and "AAbin" objects).

gap

the character used to represent gaps in the alignment matrix. Ignored for "DNAbin" or "AAbin" objects. Defaults to "-" otherwise.

Value

a list of sequences of the same mode and class as the input alignment (ie "DNAbin", "AAbin", or plain ASCII characters).

Details

unalign works in the opposite way to align, reducing a matrix of aligned sequences to a list of sequences without gaps. "DNAbin" and "AAbin" matrix objects are supported (and recommended for biological sequence data)

See Also

align.

Examples

# NOT RUN {
## Convert the woodmouse alignment in the ape package to a list of
## unaligned sequences
library(ape)
data(woodmouse)
x <- unalign(woodmouse)
# }