Expand description
Methods for inferring the site frequency spectrum from low-quality data using various forms of the expectation-maximisation algorithm.
Modules§
- em
- Expectation-maximisation (“EM”) algorithms for SFS inference.
- io
- Utilities for working with SAF files stored on disk.
- prelude
- The types required for common usage.
- saf
- Site allelele frequency (“SAF”) likelihoods.
- sfs
- Multi-dimensional site frequency spectra (“SFS”).
Macros§
- saf1d
- Creates a SAF matrix of a single population.
- saf2d
- Creates a joint SAF matrix of two populations.
- sfs1d
- Creates an unnormalised 1D SFS.
- sfs2d
- Creates an unnormalised 2D SFS.
Functions§
- set_
threads - Sets the number of threads to use for parallelization.