seqinr (version 3.1-2)

as.alignment: Constructor for class alignment

Description

Returns an object of (S3) class alignment.

Usage

as.alignment(nb = NULL, nam = NULL, seq = NULL, com = NULL)

Arguments

nb

integer. The number of sequences in the alignment.

nam

vector of nb character strings. The sequence names.

seq

vector of nb character strings. The aligned sequences.

com

vector of nb character strings. The comments about sequences.

Value

• An object of class alignment which is a list with the following components:
• nb
  the number of aligned sequences
• nam
  a vector of strings containing the names of the aligned sequences
• seq
  a vector of strings containing the aligned sequences
• com
  a vector of strings containing the commentaries for each sequence or NA if there are no comments

References

citation("seqinr")

See Also

read.alignment, as.matrix.alignment, read.fasta, write.fasta, reverse.align, dist.alignment.

Examples

as.alignment(nb = 2, nam = c("one", "two"), 
  seq = c("-ACGT", "GACG-"), com = c("un", "deux"))