asIBDNe (Ancestry-specific IBD-based estimation of Ne)

Citation: Browning SR, Browning BL, et al. Ancestry-specific recent effective population size in the Americas. PLoS Genet. 2018. 14:e1007385.

Links to programs, utilities and scripts:
IBDNE, BEAGLE (for phasing), Refined IBD (for IBD detection, including gapfilling), Beagle Utilities (for filtercolumns.jar), RFMix, python scripts and script for running RFMix (for,, and run_rfmix).

Link to simulated data. This file has the sequence of commands that can be used to replicate the simulated data analysis, using these data and the above-linked scripts.

If you find problems with these commands/scripts, please contact Sharon Browning:

Technical issues

For some reason, tends to download as an html rather than a txt file. If this happens to you, instead download constrecomb.txt and rename it to before runing the scripts.