ident.seq: Identify or delete identical DNA sequences

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description

This functions identifies identical sequences in an alignment of DNA sequences. In each subset of identical sequences all but the first identical sequences are deleted from the alignment.

Usage

ident.seq(x, quiet = TRUE)

Arguments

x	An object of class DNAbin.
quiet	Logical, if TRUE number and name the deleted sequences are printed out on the console

Value

An object of class DNAbin.

Author(s)

Christoph Heibl

See Also

delete.empty.cells to identify and delete empty rows and columns, i.e., rows and columns containing only Ns.

Examples

data(woodmouse)
seq <- woodmouse[c(1, 2, 3, 3 , 3, 4, 4), ]
seq2 <- ident.seq(seq, quiet = FALSE)
rownames(seq2)

fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.