The function transforms dna2codon DNA sequences to codon sequences,
codon2dna transform the other way. dna2codon translates
nucleotide to amino acids using the function trans.
Usage
dna2codon(x, codonstart = 1, code = 1, ambiguity = "---", ...)
codon2dna(x)
dna2aa(x, codonstart = 1, code = 1)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.
See also
trans, phyDat and the chapter 4 in the
vignette("phangorn-specials", package="phangorn")
Author
Klaus Schliep klaus.schliep@gmail.com
Examples
data(Laurasiatherian)
class(Laurasiatherian)
#> [1] "phyDat"
Laurasiatherian
#> 47 sequences with 3179 character and 1605 different site patterns.
#> The states are a c g t
dna2codon(Laurasiatherian)
#> 47 sequences with 1059 character and 914 different site patterns.
#> The states are aaa aac aag aat aca acc acg act aga agc agg agt ata atc atg att caa cac cag cat cca ccc ccg cct cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat gca gcc gcg gct gga ggc ggg ggt gta gtc gtg gtt tac tat tca tcc tcg tct tgc tgg tgt tta ttc ttg ttt