This function displays the polymorphic sites (base substitutions and indels) between the two sequences.
## S4 method for signature 'Dna' polymorp(x,pair,indels="sic")
an object of class
a vector of integers in the range [1,nrow(x)] of length two, specifying sequence pair.
the indel coding method to be used. This must be one of "sic", "5th" or "missing". Any unambiguous substring can be given. See
a list with two components:
a list of matrices of the indel regions if
indels=="sic". The component names of the list gives the position of the indels.
a list of matrices of the base substitutions. If
indels=="5th", each gap is treated as a base substitution. The component names of the list gives the position of the base substitutions.
signature(x = "Dna")
Showing base substitutions and indels between the two sequences.
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data("dna.obj") x<-dna.obj ## Showing base substitutions and indels between seq1 and seq6. # gaps are coded following the simple indel coding method polymorp(x,c(1,6),indels="s") # gaps are coded as a fifth state character polymorp(x,c(1,6),indels="5") # gaps are treated as missing character polymorp(x,c(1,6),indels="m")
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