Consider a random real tree whose leaf set, or boundary, is endowed with a finite mass measure. Each element of the tree is further given a type, or allele, inherited from the most recent atom of a random point measure (infinitely-many-allele model) on the skeleton of the tree. The partition of the boundary into distinct alleles is the so-called allelic partition. In this paper, we are interested in the infinite trees generated by super-critical, possibly time-inhomogeneous, binary branching processes, and in their boundary, which is the set of particles 'co-existing at infinity'. We prove that any such tree can be mapped to a random, compact ultrametric tree called coalescent point process, endowed with a 'uniform' measure on its boundary which is the limit as t → ∞ of the properly rescaled counting measure of the population at time t. We prove that the clonal (i.e., carrying the same allele as the root) part of the boundary is a regenerative set that we characterize. We then study the allelic partition of the boundary through the measures of its blocks. We also study the dynamics of the clonal subtree, which is a Markovian increasing tree process as mutations are removed.