Rooting of phylogenetic trees is an important task, not only in evolutionary biology, but also in historical linguistics. So far, however, different rooting methods have not yet been sufficiently tested on linguistics data. Given that a new method for the automatic rooting of phylogenetic trees has been presented recently in biology, it seemed to be a good occasion to test in detail how well this new method works in comparison with alternative methods.
A major problem for data reuse in computer-assisted historical linguistics, especially when employing data collected with no computational workflows in mind, is linking datasets in terms of the meanings of the words (or, technically, “forms”) they carry. Just as linking languages across different datasets is not as straightforward as one might naively assume, demanding a complex reference catalog such as Glottolog, linking the concepts used in a wordlist (a “concept list”) to our Concepticon project might well be the most intensive task in preparing a dataset for cross-linguistic studies.
Following up on my announcement to present in more detail how the algorithms for automatic correspondence pattern detection can be applied, this post introduces the preliminary preparations needed to run a first experiment with aligned data. In order to avoid that we have to align a dataset completely from scratch, we make use of already aligned data from the Tableaux Phonétiques des Patois Suisses Romands by Gauchat et al. (1925), which were originally aligned for the study in List (2014) and later published as part of the Benchmark Database of Phonetic Alignments(List and Prokić 2014). In this post, I will introduce how we can harvest the alignments from this dataset with help of LingPy, and later analyze them with help of the sound correspondence pattern algorithms.