Alignments and Phylogenetic Reconstruction

Alignments and phylogenetic reconstruction are the two major steps of evolutionary analysis in biology. In linguistics, instead of alignments, assemblies of cognate words are used. Essentially, however, we find a similar situation in both disciplines, in so far as the first step in the workflow (alignment or cognate assessment) is usually carried out manually or at least manually adjusted, while the second step (phylogenetic reconstruction) is completely trusted to the machines. I reflect about this situation, trying to show why alignments are so difficult in historical linguistics, and why we should be a bit careful with what part of our analyses we should exclusively leave to humans or machines in another blog post for David Morrisons blog The Genealogical World of Phylogenetic Networks, with the title "Alignments and phylogenetic reconstruction in linguistics and biology".