Hands-on Labs
Phylogenetic Methods in Historical Linguistics · Naxos 2026
All three labs run inside your web browser. There is no Python to install, no R, no MrBayes, no account to create, and nothing you write is sent to a server.
Open a lab, edit any code cell, and press Run Code. If you break something, press Start Over.
(If you want to run them on your own machine afterwards, the code is standard Python and R. You do not need to do so during the session, and you should not try.)
The three labs
They tell one story, in order.
Lab 1: Cognate Detection with LingPy
Where the character matrix comes from. We take 13 Indo-European languages with expert cognate judgements, run LexStat’s automatic cognate detection against them, and score the result. Precision is 0.97, but recall only 0.70. Why it misses a third of the cognates is arguably the most instructive part of the lab.
Runs in the browser. Python, about 10 seconds to load.
Lab 2: Bayesian Phylogenetics with MrBayes
What we build on top of that matrix, and whether to believe it. MrBayes has been run in advance, since a chain does not finish inside a lecture slot. The lab therefore covers the part that matters in practice: reading the output and deciding whether to trust it. We look at convergence diagnostics, traces, and the consensus tree. We also see that the recommended default branch-length prior fails on this data, while the supposedly discredited one works.
Runs in the browser. R, about a minute to load.
Lab 3: Beyond Cognacy
How to avoid the bottleneck. Cognate coding is expensive, and it does not scale beyond a handful of families. We therefore build a tree without deciding what is cognate with what. Instead of asking a specialist, we align the words and ask only whether a language has sound s at aligned position i. This is the method behind the 3,397-language world tree of Jäger (2026), applied here to our 13 languages.
Runs in the browser. Python and R.
If the network fails
Everything runs client-side, so a lab keeps working once its setup cell has finished, even if the WiFi drops. Open all three at the start of the session, wait for each to print ready, and you are insulated.
Afterwards
The labs are yours to keep. They will still be here, and they will still run, with no setup, on any machine with a browser.