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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

Versioning


No version available

Documentation


Maintainer


  • person_outline Tanja Stadler

Publication for TreePar

TreePar citations

 (22)
library_books

Estimating Age Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies

2017
Syst Biol
PMCID: 5920349
PMID: 29069434
DOI: 10.1093/sysbio/syx082

[…] nces and was analyzed under the same settings used for the full data set.We then analyzed a dated phylogeny of all extant carnivores comprising 286 species, with crown age at about 65 Ma () using the TreePar package to identify evidence of ADE. We ran maximum likelihood optimizations under the model with gamma-distributed longevities (i.e., ADE) and exponentially distributed longevities (age-indep […]

library_books

Insight into Central Asian flora from the Cenozoic Tianshan montane origin and radiation of Lagochilus (Lamiaceae)

2017
PLoS One
PMCID: 5606930
PMID: 28931016
DOI: 10.1371/journal.pone.0178389

[…] Model 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 proces […]

library_books

No evidence for the radiation time lag model after whole genome duplications in Teleostei

2017
PLoS One
PMCID: 5398669
PMID: 28426792
DOI: 10.1371/journal.pone.0176384

[…] o-evolutionary 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 actinopterygia […]

call_split

Estimating shifts in diversification rates based on higher level phylogenies

2016
PMCID: 5095187
PMID: 27703054
DOI: 10.1098/rsbl.2016.0273
call_split See protocol

[…] roduced.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 ma […]

library_books

Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae)

2016
BMC Evol Biol
PMCID: 5031269
PMID: 27654122
DOI: 10.1186/s12862-016-0758-1

[…] circumtatrica, Rh. gratianopolitana, Rh. beskidensis, Rh. semicolorata, Rh. taurisca, Rh. puytoraci, Rh. iridina, Rh. picteti, and Rh. fonticola.Fig. 3Speciation and extinction rates calculated using TreePar (bd.shifts.optim() function) and used for tree simulations with CorSiM were λ = 0.24 and μ = 0.08. The data set completed by simulation (Fig. ) was characterised by γ = 1.07 (SD 0.44, one-tail […]

call_split

Natural Constraints to Species Diversification

2016
PLoS Biol
PMCID: 4978419
PMID: 27505866
DOI: 10.1371/journal.pbio.1002532
call_split See protocol

[…] inear 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 in the hist […]


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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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