addMSA: Add matching sequence alignment to the tree

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

Add matching sequence alignment to the tree

Description

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, ...)

## S3 method for class 'phylo'
addMSA(
  tree,
  msaPath = "",
  msaFormat = c("fasta", "clustal", "phylip", "mase", "msf"),
  alignment = NULL,
  seqType = c("AA", "DNA", "RNA"),
  ...
)

## S3 method for class 'treedata'
addMSA(tree, ...)

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. The tree is supposed to be fully resolved (bifurcated) and will be resolved by multi2di if is.binary gives FALSE.
...	Other arguments.
msaPath	The file path to the multiple sequence alignment file.
msaFormat	The format of the multiple sequence alignment file. The internal uses the read.alignment from seqinr package to parse the sequence alignment. The default is "fasta" and it also accepts "clustal", "phylip", "mase", "msf".
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
seqType	The type of the sequence in the alignment file. The default is "AA" for amino acid. The other options are "DNA" and "RNA".

Value

Since 1.5.12, the function returns a phyMSAmatched object to avoid S3 methods used on phylo (better encapsulation).

See Also

read.alignment

Examples

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

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.