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TreePar specifications

Information


Unique identifier OMICS_13069
Name TreePar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.3
Stability Stable
Requirements
Matrix, ape, deSolve, subplex, TreeSim(≥2.1)
Source code URL https://cran.r-project.org/src/contrib/TreePar_3.3.tar.gz
Maintained Yes

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Maintainer


  • person_outline Tanja Stadler <>

Publication for TreePar

TreePar in publications

 (20)
PMCID: 5606930
PMID: 28931016
DOI: 10.1371/journal.pone.0178389

[…] selection was based on the difference in aic scores between the best-fitting rate-constant and rate-variable models (δaicrc). the calculations were performed using laser 2.3 []. we further used treepar [] to identify the locations of temporal shifts in diversification rates of lagochilus. treepar analyses were run with a grid setting of 0.1 million years with both yule and birth-death […]

PMCID: 5398669
PMID: 28426792
DOI: 10.1371/journal.pone.0176384

[…] rate fitting as a function of time, to compare the dynamics of diversification and highlight potential signs of delayed rise after the paleopolyploidy., the first method that we used was treepar [], which can estimate diversification rates across time ranges on a phylogenetic tree. we have previously shown that this method is robust to mass extinctions, as have affected […]

PMCID: 5394666
PMID: 28404776
DOI: 10.1098/rspb.2017.0095

[…] we investigated diversification dynamics in the fungus-farming ants using two approaches. we tested for significant shifts in diversification rates across the entire tree using the r package treepar [], which is an ml-based program that allows for non-constant diversification rates and incomplete taxon sampling. we also tested for rate shifts among lineages using the bayesian program […]

PMCID: 5095187
PMID: 27703054
DOI: 10.1098/rsbl.2016.0273

[…] for all trees, maximum-likelihood estimates of diversification rate λ − μ and turnover μ/λ before and after the rate shift, together with the time of the rate shifts, have been obtained using treepar v. 3.3 function bd.shifts.optim [] with the ‘groups’ option. this function employs equation (3.1) below., the code required to perform our analyses is provided in the electronic supplementary […]

PMCID: 4978419
PMID: 27505866
DOI: 10.1371/journal.pbio.1002532

[…] and exponential diversity dependence of speciation rates, exponential temperature dependence, and sgd. the mass extinction model was fitted using the |bd.shifts.optim| function in the r package treepar, which maximizes the likelihood of a model with constant speciation and extinction rates and one or more sampling events (i.e., mass extinctions) at discrete time points t1,t2,…,tn […]


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TreePar institution(s)
Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, Zurich, Switzerland
TreePar funding source(s)
Funding for this work came from Eidgenössiche Technische Hochschule, Zurich.

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