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(sec_introduction)=

# Introduction

This is the documentation for pyslim, a Python API
for reading and modifying {ref}`tskit<tskit:sec_introduction>` tree sequence files
produced by [SLiM](https://messerlab.org/slim/), 
or modifying files produced by other programs (e.g.,
{ref}`msprime<msprime:sec_intro>`,
[fwdpy11](https://fwdpy11.readthedocs.io/en/stable/pages/tsoverview.html),
and [tsinfer](https://tsinfer.readthedocs.io/)) 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 {ref}`sec_overview`
for a description of what (and *who*)
SLiM records in the tree sequence.
Next, the {ref}`sec_tutorial` walks through the common workflows.