R: Translate nucleic acid sequences into codons

dna2codon {phangorn} | R Documentation

## Translate nucleic acid sequences into codons

### Description

The function transforms `dna2codon` DNA sequences to codon sequences, `codon2dna` transform the other way.

### Usage

    dna2codon(x, codonstart = 1, code = 1, ambiguity = "---", ...)

    codon2dna(x)

### Arguments

`x` | An object containing sequences.
`codonstart` | an integer giving where to start the translation. This should be 1, 2, or 3, but larger values are accepted and have for effect to start the translation further within the sequence.
`code` | The ncbi genetic code number for translation (see details). By default the standard genetic code is used.
`ambiguity` | character for ambiguous character and no contrast is provided.
`...` | further arguments passed to or from other methods.

### Details

The following genetic codes are described here. The number preceding each corresponds to the code argument.

1 | standard
2 | vertebrate.mitochondrial
3 | yeast.mitochondrial
4 | protozoan.mitochondrial+mycoplasma
5 | invertebrate.mitochondrial
6 | ciliate+dasycladaceal
9 | echinoderm+flatworm.mitochondrial
10 | euplotid
11 | bacterial+plantplastid
12 | alternativeyeast
13 | ascidian.mitochondrial
14 | alternativeflatworm.mitochondrial
15 | blepharism
16 | chlorophycean.mitochondrial
21 | trematode.mitochondrial
22 | scenedesmus.mitochondrial
23 | thraustochytrium.mitochondria
24 | Pterobranchia.mitochondrial
25 | CandidateDivision.SR1+Gracilibacteria
26 | Pachysolen.tannophilus

Alignment gaps are simply and base ambiguities are currently ignored and sites containing these are deleted.

### Value

The functions return an object of class `phyDat`.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### References

https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes

### See Also

`trans`, `phyDat` and the chapter 4 in the `vignette("phangorn-specials", package="phangorn")`

### Examples

    data(Laurasiatherian)
    class(Laurasiatherian)
    Laurasiatherian
    dna2codon(Laurasiatherian)

[Package phangorn version 2.6.2 Index]