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MultiTypeTree specifications


Unique identifier OMICS_13060
Name MultiTypeTree
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL
Maintained Yes


No version available



  • person_outline Timothy Vaughan

Publication for MultiTypeTree

MultiTypeTree citations


MERS CoV spillover at the camel human interface

PMCID: 5777824
PMID: 29336306
DOI: 10.7554/eLife.31257.038

[…] For our primary analysis, the MultiTypeTree module () of BEAST v2.4.3 () was used to specify a structured coalescent model with two demes – humans and camels. At time of writing structured population models are available in BEAST […]


The Structured Coalescent and Its Approximations

Mol Biol Evol
PMCID: 5850743
PMID: 28666382
DOI: 10.1093/molbev/msx186

[…] in of an epidemic. Here, we show on one fixed tree how the exact structured coalescent compares in the inference of the root state to its approximations. We additionally inferred the root state using MultiTypeTree (), which uses MCMC to sample lineage states and does not rely on approximations, to obtain a reference root state probability (). We inferred the probability of the root being in either […]


New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

PLoS Genet
PMCID: 4534465
PMID: 26267488
DOI: 10.1371/journal.pgen.1005421

[…] , T represents the genealogy, μ the nucleotide substitution rate matrix and M the migration history of lineages in the tree, i.e. the timing, source, sink and lineage involved in each migration event.MultiTypeTree (MTT) is a method implemented in BEAST2 for estimating the parameters of the structured coalescent by Bayesian inference []. Formally, the target of inference is the posterior distributi […]


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MultiTypeTree institution(s)
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand; Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland; Department of Computer Science, University of Auckland, Auckland, New Zealand
MultiTypeTree funding source(s)
This work was supported by the Allan Wilson Centre for Molecular Ecology and Evolution; Royal Society of New Zealand Marsden grant [UOA0809]; Rutherford Discovery Fellowship from the Royal Society of New Zealand.

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