addMSA {sitePath}R Documentation

Prepare data for sitePath analysis

Description

sitePath requires both tree and sequence alignment to do the analysis. addMSA wraps read.alignment function in seqinr package and helps match names in tree and sequence alignment. Either provide the file path to an alignment file and its format or an alignment object from the return of read.alignment function. If both the file path and alignment object are given, the function will use the sequence in the alignment file.

Usage

addMSA(tree, msaPath = "", msaFormat = "", alignment = NULL)

Arguments

tree

a phylo object. This commonly can be from tree parsing function in ape or ggtree. All the tip.label should be found in the sequence alignment.

msaPath

The file path to the multiple sequence alignment file

msaFormat

The format of the multiple sequence alignment file

alignment

an alignment object. This commonly can be from sequence parsing function in the seqinr package. Sequence names in the alignment should include all tip.label in the tree

Value

addMSA returns a phylo object with matched multiple sequence alignment

Examples

data(zikv_tree)
msaPath <- system.file('extdata', 'ZIKV.fasta', package = 'sitePath')
addMSA(zikv_tree, msaPath = msaPath, msaFormat = 'fasta')

[Package sitePath version 1.4.2 Index]