rphast (version 1.0)

is.ordered.msa: MSA is Ordered?

Description

Determines if an MSA object represents an ordered alignment.

Usage

is.ordered.msa(msa)

Arguments

msa

an MSA object

Value

• a boolean indicating whether the columns are in order

Examples

m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"))
is.ordered.msa(m)
m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"), is.ordered=FALSE)
is.ordered.msa(m)