add.gaps: Add gap-only sequences for missing data

In thibautjombart/apex: Phylogenetic Methods for Multiple Gene Data

Add gap-only sequences for missing data

Description

In multidna and multiphyDat, some individuals may not be sequenced for all genes. The generic function add.gaps has method for both objects; it identifies the missing sequences, and adds gap-only sequences to the alignments wherever needed.

Usage

add.gaps(x, ...)

## S4 method for signature 'multidna'
add.gaps(x, ...)

## S4 method for signature 'multiphyDat'
add.gaps(x, ...)

Arguments

x	a multidna or multiphyDat object.
...	further arguments passed to other methods (currently not used).

thibautjombart/apex documentation built on Feb. 7, 2024, 7:13 a.m.