| 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 and 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)