nonsquareDist - Calculate pairwise distances between sequences


nonsquareDist calculates all pairwise distance between a set of sequences and a subset of it.


nonsquareDist(seq, indx, dist_mat = getDNAMatrix())


character vector containing a DNA sequences. The sequence vector needs to be named.
numeric vector contating the indices (a subset of indices of seq).
Character distance matrix. Defaults to a Hamming distance matrix returned by getDNAMatrix. If gap characters, c("-", "."), are assigned a value of -1 in dist_mat then contiguous gaps of any run length, which are not present in both sequences, will be counted as a distance of 1. Meaning, indels of any length will increase the sequence distance by 1. Gap values other than -1 will return a distance that does not consider indels as a special case.


A matrix of numerical distance between each entry in seq and sequences specified by indx indices.

Note that the input subsampled indices will be ordered ascendingly. Therefore, it is necassary to assign unique names to the input sequences, seq, to recover the input order later. Row and columns names will be added accordingly.

Amino acid distance matrix may be built with getAAMatrix. Uses seqDist for calculating distances between pairs. See pairwiseEqual for generating an equivalence matrix.


# Gaps will be treated as Ns with a gap=0 distance matrix
seq <- c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C")

  A B C D
A 0 1 1 0
B 1 0 0 1
C 1 0 0 1
D 0 1 1 0

nonsquareDist(seq, indx=c(1,3), 
  A B C D
A 0 1 1 0
C 1 0 0 1