blockAlignment {spider} | R 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 |
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)))
[Package spider version 1.5.0 Index]