AdmixTools 2 Lab

ADMIXTOOLS 2 is the R package formal admixture modelling is done with in published ancient-DNA research. Normally using it means installing R, compiling the package, obtaining a genotype panel and learning its interface. This page runs the real functions on our servers against the Allen Ancient DNA Resource Human Origins panel, so you can compose a model in a form and read the output — the same `qpadm()`, `qpwave()` and f-statistic routines, not an approximation of them.

The methods available here work from allele-frequency statistics rather than coordinate distances. f2, f3, f4 and D statistics measure shared drift and treeness between population sets. qpWave asks how many independent ancestry streams are needed to relate two sets. qpAdm goes further: you give it a target, a set of candidate sources (the left set) and a set of outgroups (the right set), and it estimates each source's weight with a standard error and a z-score, plus a p-value for the model as a whole. Admixture-graph fitting searches for a tree-with-admixture topology consistent with the f-statistics.

The p-value is what makes qpAdm different in kind from a coordinate fit: it can say the proposed model is incompatible with the data, and a rejected model is the method working rather than a failure of the tool. Expect rejections, and expect the right set to matter as much as the left — outgroups are what give the test its power, and a right set too small or too closely related to your sources will accept almost anything. A weight is only meaningful if it sits several standard errors away from zero.

Limits worth knowing before you start. Runs execute on a single serialized worker, so one account may create 20 runs in a rolling 24 hours and hold 2 queued or running at once — the quota exists because each run costs real CPU that everyone else is waiting on. Analyses here operate on reference populations from the panel, not on your own genotypes; modelling your own sample as the target requires it to be merged into the panel first, which is what our paid qpAdm analysis does. A free, email-verified account is needed to run, though this page and its description are public.