dna2codon: Translate nucleic acid sequences into codons

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

Translate nucleic acid sequences into codons

Description

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.

Value

The functions return an object of class phyDat.

Author(s)

Klaus Schliep [e-mail]

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)

KlausVigo/phangorn documentation built on Nov. 5, 2024, 11 a.m.