ltg2amb: Replace leading and trailing alignment gaps with an ambiguous...

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

Replace leading and trailing alignment gaps with an ambiguous state

Description

Substitutes leading and trailing alignment gaps in aligned sequences into N (i.e., A, C, G, or T) or ?. The gaps in the middle of the sequences are left unchanged.

Usage

ltg2amb(x, amb = ifelse(attr(x, "type") == "DNA", "N", "?"), gap = "-")

Arguments

x	an object of class phyDat.
amb	character of the ambiguous state t replace the gaps.
gap	gap parameter to replace.

Value

returns an object of class phyDat.

See Also

latag2n, ancestral.pml, gap_as_state

Examples

x <- phyDat(matrix(c("-", "A", "G", "-", "T", "C"), 2, 3))
y <- ltg2amb(x)
image(x)
image(y)

KlausVigo/phangorn documentation built on June 23, 2024, 10:49 p.m.