Comparing branching and axillary flowering patterns accurately is a major issue both in botany and in various agronomic contexts. Data take the form of sequences which naturally represent the underlying structural information of branching and axillary flowering patterns. Various comparison methods are proposed based either on sequence alignment or on the computation of dissimilarity measures between (hidden) Markovian models built from sets of sequences. Sequence alignment is a natural complement to the exploratory tools and statistical models proposed in Guédon et al. (J. Theor. Biol. 212 (2001) 481) with the distinctive feature of applying to individual sequences. Comparison methods may also be used to reveal some grouping within a set of sequences or to evaluate the strength of a predefined grouping of sequences. The proposed approach is illustrated by examples corresponding to different plant species and different biological or agronomic objectives.