blockAlignmentR Documentation

Make all sequences the same length

Description

Coerces all sequences in a DNAbin object to the same length.

Usage

blockAlignment(DNAbin, mode = "shortest", range = NULL, fill = "")

Arguments

DNAbin

An object of class DNAbin

mode

Character vector. Options of "shortest" or "longest"

range

Numeric vector of length 2. Index of the bases where the new alignment should begin and end

fill

Character to fill the extra bases in short sequences. Default of "" (blank). Recommend that only "-" (gap) or "?" be used

Details

When mode = "shortest", the alignment is truncated at the length of the shortest sequence. When mode = "longest", the alignment is extended to the end of the longest sequence, with shorter sequences filled in with "fill"s.

Value

A DNAbin object in matrix format.

Author(s)

Samuel Brown <s_d_j_brown@hotmail.com>

Examples


data(salticidae)
salticidae
blockAlignment(salticidae)
blockAlignment(salticidae, mode = "longest")
blockAlignment(salticidae, mode = NULL, range = c(200, 600))

graphics::image(blockAlignment(salticidae))
graphics::image(blockAlignment(salticidae, mode = "longest"))
graphics::image(blockAlignment(salticidae, mode = NULL, range = c(200, 600)))