The asymmetric tropical distance is a distance measure on the tropical torus $\mathbb{R}^n/\mathbb{R}\mathbf{1}$ and in particular on the Bergman fan $B(K_N) \subseteq \mathbb{R}^{\binom{N}{2}}/\mathbb{R}\mathbf{1}$ of the complete graphical matroid. In this paper, we define and analyse a clustering algorithm for equidistant phylogenetic trees based on this distance, using the correspondence between $B(K_N)$ and the space of equidistant trees with $N$ leaves.