Codon Alignments using PAL2NAL

This function takes a protein alignment and the corresponding coding sequences as fasta files and computes the corresponding codon alignment based on the models specified in the PAL2NAL program.

codon_aln(
  file_aln,
  file_nuc,
  format = "clustal",
  tool = "pal2nal",
  params = NULL,
  codon_aln_name = NULL,
  get_aln = FALSE,
  quiet = FALSE
)

Arguments

file_aln	a character string specifying the path to the file storing the protein alignment in CLUSTAL or FASTA format.
file_nuc	a character string specifying the path to the file storing the coding sequences in multiple FASTA format.
format	a character string specifying the file format used to store the codon alignment, e.g. "fasta", "clustal".
tool	a character string specifying the program that should be used e.g. "pal2nal".
params	a character string specifying additional parameters that shall be passed to PAL2NAL. For example params = "-codontable 2" would specify a codon table: vertebrate mitochondrial code instead if the universal code (default). The default value is params = NULL. Default is codon_aln_name = NULL denoting a default name: 'tool_name.aln' .
codon_aln_name	a character string specifying the name of the stored alignment file.
get_aln	a logical value indicating whether the produced alignment should be returned.
quiet	a logical value specifying whether a successful interface call shall be printed out.

Value

In case get_aln = TRUE an seqinr alignment object is returned.

Details

This function provides an interface between the R language and common codon alignment tools such as "PAL2NAL". Codon alignments can be used to quantify the evolutionary pressure acting on protein sequences based on dNdS estimation.

The PAL2NAL program is used to convert a multiple sequence alignment or pairwise alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon-based DNA alignment. The output codon-based DNA alignment can then be used for dNdS estimation.

The popular codon alignment tool PAL2NAL is included in this package and is being called when choosing tool = "pal2nal".

Note

The PAL2NAL program automatically checks

• If you use the same IDs are used in the protein alignment file and DNA (or mRNA) file -> in this case the sequences don't have to be in the same order

• If you don't use the same IDs are used in the protein alignment file and DNA (or mRNA) file -> you have to rearrange the IDs or sequences so that sequences in the protein alignment file and DNA (or mRNA) file have the same order

References

Mikita Suyama, David Torrents, and Peer Bork (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609-W612.

http://www.bork.embl.de/pal2nal/

http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi

http://abacus.gene.ucl.ac.uk/software/paml.html

See also

pairwise_aln, multi_aln, substitutionrate, dNdS, divergence_stratigraphy

Author

Hajk-Georg Drost

Examples

if (FALSE) {

# performing a codon alignment using PAL2NAL
codon_aln <- codon_aln(file_aln = system.file('seqs/aa_seqs.aln', package = 'homologr'),
                       file_nuc = system.file('seqs/dna_seqs.fasta', package = 'homologr'),
                       format   = "clustal",
                       tool     = "pal2nal",
                       get_aln  = TRUE)


# running PAL2NAL with additional parameters (e.g. a different codon table)
codon_aln <- codon_aln(file_aln = system.file('seqs/aa_seqs.aln', package = 'homologr'),
                       file_nuc = system.file('seqs/dna_seqs.fasta', package = 'homologr'),
                       format   = "clustal",
                       tool     = "pal2nal",
                       get_aln  = TRUE,
                       params   = "-codontable 2")

}