The function transforms dna2codon DNA sequences to codon sequences,
codon2dna transform the other way.
dna2codon(x, codonstart = 1, code = 1, ambiguity = "---", ...)codon2dna(x)
An object containing sequences.
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.
The ncbi genetic code number for translation (see details). By default the standard genetic code is used.
character for ambiguous character and no contrast is provided.
further arguments passed to or from other methods.
The functions return an object of class phyDat.
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 |
Alignment gaps and ambiguities are currently ignored and sites containing these are deleted.
https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes
trans, phyDat and the chapter 4 in the
vignette("phangorn-specials", package="phangorn")
# NOT RUN {
data(Laurasiatherian)
class(Laurasiatherian)
Laurasiatherian
dna2codon(Laurasiatherian)
# }
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