These software packages all produce or consume tree sequences in the .trees file format.

Simulate

Create tree sequences from models of biological processes

Simulate genealogical trees and genomic sequence data using population genetic models

ts = msprime.sim_ancestry(
    samples=10, 
    recombination_rate=1e-4, 
    sequence_length=1e6
)
ts = msprime.sim_mutations(ts, rate=1e-6)
Latest release: 1.2.0 1 month and 1 week ago
30 contributors

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.

initialize() {
    initializeTreeSeq();
    initializeMutationRate(1e-8);
    initializeMutationType("m1", 0.5, "e", 0.001);
    initializeGenomicElementType("g1", m1, 1.0);
    initializeGenomicElement(g1, 0, 999999);
    initializeRecombinationRate(1e-8);
}
1 { sim.addSubpop("p1", 500); }
2000 late() { sim.treeSeqOutput("out.trees"); }
Latest release: v3.7.1 4 months and 2 weeks ago
12 contributors

Forward-time simulation in Python using fwdpp

##TODO##
Latest release: 0.18.1 3 weeks and 6 days ago
4 contributors

Infer

Create tree sequences from variation data

Infer a tree sequence from genetic variation data.

sample_data = tsinfer.load("phased_sequence_data.samples")
ts = tsinfer.infer(sample_data)
Latest release: 0.2.3 2 months and 2 weeks ago
10 contributors

Infer the age of ancestral nodes in a tree sequence.

dated_ts = tsdate.date(inferred_ts)
Latest release: 0.1.5 2 weeks and 4 days ago
3 contributors

Analyse

Measure key statistics, manipulate tree sequences and their underlying tables

Population-scale genomics

ts = tskit.load("example.trees")
afs = ts.allele_frequency_spectrum()
Latest release: 0.5.0 5 days ago
30 contributors

Tools for dealing with tree sequences coming to and from SLiM.

  rts = pyslim.recapitate(ts, ancestral_Ne=10000)
Latest release: 1.0b1 3 weeks and 2 days ago
10 contributors

rust bindings for tskit!

##TODO##
Latest release: 0.9.0 1 week ago
4 contributors