About Nexju

Population geneticists test ancestry models with the ADMIXTOOLS, EIGENSOFT and DATES programs. Those programs need a Unix machine, genotype files of many gigabytes and the skill to prepare both. Nexju keeps the reference data loaded and runs the same analyses on its servers. You choose the populations from lists, and the results come back as tables and charts with their p-values, standard errors and Z-scores.

Nexju is for people who want to test a model, not only read an estimate: students, researchers, genetic genealogists and readers of ancient DNA papers. A result is a statistical model of ancestry. It is not an ethnicity estimate, a genealogical proof or health information.

Analyses run on the Allen Ancient DNA Resource (AADR) (Mallick et al. 2024), the curated dataset of published ancient and present-day genomes behind most ancient DNA studies. Nexju uses release v66, on its 1240K and Human Origins SNP sets. Population labels are the AADR’s own, so a model in Nexju names the same groups as the papers do.

Each genome in the AADR comes from a published study. When you report a result, cite the AADR and the original publication of each genome you used.

Nexju runs native implementations of the published methods. Each one is checked against the reference program with fixed test data:

• f3, f4, f4-ratio, qpGraph and the qpGraph search against ADMIXTOOLS 2 version 2.0.10 (Maier et al. 2023);
• qpAdm against values from the classic ADMIXTOOLS qpAdm program;
• PCA against fixtures from EIGENSOFT smartpca;
• admixture dating against the DATES program, version 4010.

The statistics are the published ones: block-jackknife standard errors, the qpAdm and qpWave rank tests, and smartpca projection of ancient genomes. Nexju calls a qpAdm model plausible when its p-value is 0.01 or higher and every weight lies between 0 and 1.

The help guides explain each method from its primary papers, and every guide lists them under References. Where a guide describes Nexju, it describes what the product runs, with the names of its buttons and its limits. When the product changes, the guide changes with it, and its date shows the last update. Terms used across the guides are defined in the glossary.

Posts on the blog are written by Nexju users from their own runs. Each post names its author and shows the runs it uses, so a reader can check the models behind it.

A raw data file you upload is converted on Nexju’s servers to the format of the reference data and is used only for the analyses you request. Your uploads are visible only to you. Nexju does not sell your DNA data, add it to shared research datasets or use it to train machine-learning models, and you can delete a file at any time. An AI assistant connected through the Nexju MCP server refers to an upload by its ID and never receives your genotypes. The Privacy Policy gives the details.

Write to [email protected] with questions, corrections to a guide or a problem with a run.

• Mallick S. et al. 2024. The Allen Ancient DNA Resource (AADR): a curated compendium of ancient human genomes. Scientific Data 11. doi:10.1038/s41597-024-03031-7
• Maier R. et al. 2023. On the limits of fitting complex models of population history to f-statistics. eLife 12. doi:10.7554/eLife.85492
• Patterson N. et al. 2012. Ancient admixture in human history. Genetics 192. doi:10.1534/genetics.112.145037