fastDistAA: Faster calculation of pairwise distances between amino acid sequences of the same length
Description
fastDistAA calculates all pairwise distances among a set of amino acid sequences of the same length.
Amino acid sequences may contain the 20 standard amino acid characters and four special characters: (X, ., -, *).
The characters X, -, and . match any character, whereas standard amino acids and stop codon * match only themselves.
Usage
fastDistAA(seqs)
Value
Packed lower triangular matrix of distance between each entry in seq.
If seq is a named vector, row and columns names will be added
accordingly.
Arguments
seqs
character vector containing an amino acid sequences.