Introduction

This is the documentation for pyslim, a Python API for reading and modifying tskit tree sequence files produced by SLiM, or modifying files produced by other programs (e.g., msprime, fwdpy11, and tsinfer) for use in SLiM.

SLiM can read and write tree sequences, which store genetic genealogies for entire populations. These can be used to efficiently encode both the state of the population at various points during a simulation as well as the complete genomic ancestry. Furthermore, SLiM can “load” a saved tree sequence file to recreate the exact state of the population at the time it was saved. To do this, SLiM stores some additional information in the basic tree sequence file.

First, you probably want to read the Overview for a description of what (and who) SLiM records in the tree sequence. Next, the Tutorials walks through the common workflows.