tskit-dev projects
tskit
Documentation
tskit-dev/tskit
Population-scale genomics
ts = tskit.load("example.trees")
afs = ts.allele_frequency_spectrum()
msprime
Documentation
Publication
tskit-dev/msprime
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)
tsinfer
Documentation
Publication
tskit-dev/tsinfer
Infer a tree sequence from genetic variation data.
sample_data = tsinfer.load(
"phased_sequence_data.samples"
)
ts = tsinfer.infer(sample_data)
tsdate
Documentation
Publication
tskit-dev/tsdate
Infer the age of ancestral nodes in a tree sequence.
dated_ts = tsdate.date(inferred_ts)pyslim
Documentation tskit-dev/pyslim
Tools for dealing with tree sequences coming to and from SLiM.
rts = pyslim.recapitate(
ts,
ancestral_Ne=10000
)
tskit-rust
Documentation
tskit-dev/tskit-rust
Rust bindings for the tskit library
let treeseq = tskit::TreeSequence::load(
&treefile
).unwrap();
let mut tree_iterator =
treeseq.tree_iterator(
tskit::TreeFlags::default()
).unwrap();
while let Some(tree) =
tree_iterator.next() {
...
}Ecosystem projects
SLiM
SLiM
Website
Documentation
Publication
MesserLab/SLiM
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
);
initializeRecombinationRate(1e-8);
}
1 early() { sim.addSubpop("p1", 500); }
2000 late() {
sim.treeSeqOutput("out.trees");
}fwdpy11
Documentation molpopgen/fwdpy11
Forward-time simulation in Python using fwdpp
pop = fwdpy11.DiploidPopulation(
100, 1000.0
)
p = {
"nregions": [],
"rates": (0.0, 1e-3, None),
"prune_selected": False,
"demography":
fwdpy11.DiscreteDemography(),
"simlen": 10 * pop.N + 200,
...
}
params = fwdpy11.ModelParams(**p)
fwdpy11.evolvets(rng, pop, params)stdpopsim
Documentation Publication popsim-consortium/stdpopsim
A library of standard population genetic models
species = stdpopsim.get_species(
"HomSap"
)
model = species.get_demographic_model(
"OutOfAfrica_3G09"
)
contig = species.get_contig("chr22")
samples = {
"YRI": 5,
"CHB": 5,
"CEU": 0
}
engine = stdpopsim.get_engine(
"msprime"
)
ts = engine.simulate(
model, contig, samples
)