We apply to the task of linguistic phylogenetic inference a successful cognate identification learning model based on PAM-like matrices. We train our system and we employ the learned parameters for measuring the lexical distance between languages. We estimate phylogenetic trees using distance-based methods on an Indo-European database. Our results reproduce correctly all the established major language groups present in the dataset, are compatible with the Indo-European benchmark tree and include also some of the supported higher-level structures. We review and compare other studies reported in the literature with respect to recognised aspects of Indo-European history.