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MultiTypeTree specifications

Information


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 https://codeload.github.com/tgvaughan/MultiTypeTree/zip/master
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Timothy Vaughan

Publication for MultiTypeTree

MultiTypeTree citations

 (3)
library_books

MERS CoV spillover at the camel human interface

2018
eLife
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 […]

library_books

The Structured Coalescent and Its Approximations

2017
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 […]

library_books

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

2015
PLoS Genet
PMCID: 4534465
PMID: 26267488
DOI: 10.1371/journal.pgen.1005421

[…] ers of primary interest. We implement this approach, called BASTA (BAyesian STructured coalescent Approximation), in the Bayesian phylogenetic package BEAST2 []. We compare its performance to DTA and MultiTypeTree (MTT, a recent Bayesian structured coalescent software, see []) using simulations based on the structured coalescent.We illustrate the use of the method to reconstruct transmission dynam […]


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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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