These software packages all produce or consume tree sequences in the
.trees file format.
Create tree sequences from models of biological processes
Simulate genealogical trees and genomic sequence data using population genetic models
SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.
Create tree sequences from variation data
Infer a tree sequence from genetic variation data.
Measure key statistics, manipulate tree sequences and their underlying tables
Tools for dealing with tree sequences coming to and from SLiM.