narrowingWindow: Make all sequences the same length

In spiderDev: Species Identity and Evolution in R--development

Description

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

Usage

narrowingWindow(DNAbin, interval = 10)
narrowingWindow2(DNAbin, interval = 1, direction = "left")
giveMeThePicture(DNAbin)

Arguments

DNAbin	An object of class DNAbin
interval	Numeric. Size of steps by which the alignment should be trimmed.
direction	Character vector. Options of "left", "right" or "both"

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 "N"s.

Value

narrowingWindow and narrowingWindow2 return lists of DNAbin objects.

giveMeThePicture returns a picture of the GC content as the alignment is trimmed.

Author(s)

Samuel Brown <[e-mail]>

Examples

data(dolomedes)
narrowingWindow(dolomedes)
narrowingWindow2(dolomedes)
giveMeThePicture(dolomedes)

spiderDev documentation built on May 2, 2019, 5:23 p.m.