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