phyMSAmatched {sitePath} | R Documentation

## 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')

[Package sitePath version 1.6.6 Index]