Are phylogenetic tree construction algorithms any different than general clustering algorithms?
One difference is that phylogenetic tree construction algorithms will typically try to jointly estimate the tree and the transition parameters.  A general clustering algorithm might assume that a difference in one feature would make the same contribution to 'distance' between clusters as a difference in another feature. In phylogenetic tree construction, it is explicit that not all differences between taxa represent the same evolutionary distance between taxa, and the parameters governing the distribution of distance/difference may be jointly estimated with the tree.