{smcl} {* Copyright 2007-2011 Brendan Halpin brendan.halpin@ul.ie } {* Distribution is permitted under the terms of the GNU General Public Licence } {* 17July2015}{...} {cmd:help hamming} {hline} {title:Title} {p2colset 5 17 23 2}{...} {p2col:{hi:hamming} {hline 2}}Calculate inter-sequence distances using Hamming distance{p_end} {p2colreset}{...} {title:Syntax} {p 8 17 2} {cmd:hamming} {it: varlist} {cmd:,} {it:options} [option] {synoptset 22 tabbed}{...} {synopthdr:options} {synoptline} {syntab:Cost structure} {synopt :{opt subs:mat(matname)}} use {it:matname} as the substitution cost matrix{p_end} {syntab:Distances} {synopt :{opt pwd:ist(matname)}} store the pairwise distances in {it:matname}, as a symmetric matrix. Will be created or overwritten. {p_end} {syntab:Normalisation} {synopt :{opt STA:ndard}} (Optional) If "longer", normalise by the length of the sequences, if "none" do no normalisation. Defaults to "longer". {p_end} {synoptline} {p2colreset}{...} {title:Description} {pstd}{cmd:hamming} calculates Hamming distances between all pairs of sequences in the data, where {it:varlist} is a consecutive set of variables describing the elements of the sequence. Hamming distances compare sequences element by element such that the inter-sequence distance is the sum of the element-wise distances. The element-wise distances are given in the {it:subsmat()} substitution matrix. {pstd}States must be numbered as consecutive integers from 1 up, and the substitution cost matrix must be square, with dimension equal to the number of states. States must not be missing. {title:Author} {pstd}Brendan Halpin, brendan.halpin@ul.ie{p_end} {title:Examples} {phang}{cmd:. matrix scost = (0,1,2,3\1,0,1,2\2,1,0,1\3,2,1,0)}{p_end} {phang}{cmd:. hamming mon1-mon36, subsmat(scost) pwdist(dist)}{p_end} {phang}{cmd:. matrix list dist}{p_end} {phang}{cmd:. hamming mon1-mon72, subsmat(scost) pwdist(dist)}{p_end} {phang}{cmd:. matrix list dist}{p_end}