Terminal Restriction Fragment Length Polymorphism (TRFLP) is a potentially high through-put method to analyze complex microbial communities. However, comparison of multiple TRFLP profiles to identify shared and unique components of microbial communities is done manually, which is both time consuming and error prone. T-ALIGN addresses this problem.

Initially replicate profiles are compared and used to generate a single 'sample' profile containing only Terminal Restriction Fragments (TRFs) that occur in all replicate profiles. Subsequently 'sample' profiles representing different communities are compared to produce a list showing whether a TRF is present in a particular sample profile and what its relative fluorescence intensity is. The use of T-ALIGN thus allows rapid comparison of large numbers of TRFLP profiles.