LDDist is a Perl module implemented in C++ that allows the user to calculate LogDet pair-wise genetic distances for amino acid as well as nucleotide sequence data. It can handle site-to-site rate variation by treating a proportion of the sites as invariant and/or by assigning sites to different, presumably homogenous, rate categories. The rate-class assignments and invariant proportion can be set explicitly, or estimated by the program, the latter using either of two different capture-recapture methods. The assignment to rate categories in lieu of a phylogeny can be done using Shannon-Wiener index as a crude token for relative rate.