Several important symbols and their cross-appendix conventions are collected below.
| Symbol | Meaning | First defined |
| \(\insrate , \delrate \) | TKF insertion / deletion rates (per link) | §A |
| \(\ext \) | TKF92 fragment-extension probability | §A |
| \(\alphabet \) | residue alphabet (\(A = |\alphabet | = 20\) for proteins) | §A |
| \(\eqm , \exch , \symsub \) | GTR stationary, asymmetric, exchangeability matrices | §A |
| \(\revsub \) | substitution rate matrix (generator) | §A |
| \(\dom , \frag , \class \) | domain, fragment, and substitution-class indices (MixDom) | §C |
| \(\eta _s\) | per-site gamma rate multiplier | §D |
| \(z_s, c_s, h_{cc'}\) | key, site-class, Potts-atom indices (TKF-DP) | §D |
| \(\alpha _z, \alpha _c, \alpha _H\) | key/class/atom Dirichlet-process concentrations | §D |
| \(\Q , \Hh \) | generator and Potts coupling tensor | §D |
| \(\tkftrans \) | TKF91 Pair HMM transition matrix | §A |
| \(\exptrans \) | exploded \(7{\times }7\) MixDom top-level transitions with null states | §C |
| \(\nonemptytrans \) | effective \(5{\times }5\) MixDom top-level matrix (nulls summed out) | §C |
| \(\transnest \) | final nested MixDom Pair HMM transition matrix | §C |
| \(N_a, N_g\) | alive / gravestone counts (TKF-DP) | §D |
| \(F_0, F_1, F_2\) | TKF92 Pair HMM 0/1/2-cell marginal partition functions | §E |
| \(\pi _{\!M}\) | CRP partition of Match cells (infinite Pair HMM) | §E |