addMSA {sitePath} | R Documentation |
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.
addMSA(tree, msaPath = "", msaFormat = "", alignment = NULL)
tree |
a |
msaPath |
The file path to the multiple sequence alignment file |
msaFormat |
The format of the multiple sequence alignment file |
alignment |
an |
addMSA
returns a phylo
object with matched
multiple sequence alignment
data(zikv_tree) msaPath <- system.file('extdata', 'ZIKV.fasta', package = 'sitePath') addMSA(zikv_tree, msaPath = msaPath, msaFormat = 'fasta')