python inference.py --times example/example --out example/out

where

example/example.timeb is a binary file containing derived/ancestral coalescence times for the SNP of interest. These are estimated using Relate v1.1 [Speidel, et al. Nat. Gen. 2019] and processed using the extract_coals.py script.

If you use this program, please cite:

Stern, et al. Plos Gen. (2019) (doi: 10.1371/journal.pgen.1008384)

Please visit the Wiki pages to find tutorials of how to:

1. Run Relate

2. Run clues & command-line options (incl. incorporating aDNA samples)

3. Plot the output of clues (ie, plot frequency trajectories)

clues has developed for python 3; use python 2 at your own risk (visit the Issues section for tips on using python 2).

The programs require the following dependencies, which can be installed using conda/pip: numba, progressbar, biopython

To find the previous version of clues, which uses ARGweaver output (Rasmussen et al, 2014; Hubisz, et al, 2019; docs here), please go to https://github.com/35ajstern/clues-v0. We are no longer maintaining clues-v0