Compounding and derivation are frequent in South-East Asian languages. Consequently, words in different languages are often only partially cognate, sharing only
a few but not all morphemes. While partial cognates do not constitute a problem for the phonological reconstruction of individual morphemes, they are problematic when
it comes to phylogenetic reconstruction based on comparative wordlists. Here, we review the current practice of preparing cognate-coded wordlists and develop new approaches
that make the process of cognate annotation more transparent. Comparing four methods by which partial cognate judgments can be converted to cognate judgments
for whole words on a newly annotated dataset of 19 Chinese dialect varieties, we find that the choice of the conversion method has a large impact on the inferred tree
topologies. We conclude that scholars should take cognate judgments in languages in which compounding and derivation are frequent with great care, and recommend to
assign cognates always transparently
