Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: TreePar

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/TreePar

Estimating birth and death rates based on phylogenies
14 versions
Latest release: almost 10 years ago
1 dependent package
0 downloads

Papers Mentioning TreePar 31

10.1038/srep26340
Phylogenetic niche conservatism explains an inverse latitudinal diversity gradient in freshwater arthropods
Cited by: 41
Author(s): Jérôme Morinière, Matthew H. Van Dam, Oliver Hawlitschek, Johannes Bergsten, Mariano C. Michat, Lars Hendrich, Ignacio Ribera, Emmanuel F. A. Toussaint, Michael Balke
Software Mentions: 12
Published: over 8 years ago
10.1016/j.epidem.2014.04.003
OutbreakTools: A new platform for disease outbreak analysis using the R software
Cited by: 37
Author(s): Thibaut Jombart, David M. Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Caitlin Collins, Anne Cori, Xavier Didelot, Christophe Fraser, Simon D. W. Frost, Niel Hens, Joseph Hugues, Michael Höhle, Lulla Opatowski, Andrew Rambaut, Oliver Ratmann, Samuel Soubeyrand, Marc A. Suchard, Jacco Wallinga, Rolf J. F. Ypma, Neil M. Ferguson
Software Mentions: 11
Published: over 10 years ago
10.1186/s12862-015-0440-z
The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents
Cited by: 48
Author(s): Andrés Parada, Guillermo D’Elı́a, R. Eduardo Palma
Software Mentions: 9
Published: about 9 years ago
10.1111/evo.12483
SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS
Cited by: 34
Author(s): Cuong Q. Tang, Ulrike Obertegger, Diego Fontaneto, Timothy G. Barraclough
Software Mentions: 8
Published: over 10 years ago
10.1371/journal.pone.0095040
Evolutionary Dynamics in the Southwest Indian Ocean Marine Biodiversity Hotspot: A Perspective from the Rocky Shore Gastropod Genus Nerita
Cited by: 15
Author(s): Bautisse Postaire, J. Henrich Bruggemann, Hélène Magalon, Baptiste Faure
Software Mentions: 6
Published: over 10 years ago
10.1186/s12862-016-0758-1
Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae)
Cited by: 15
Author(s): Laurent Vuataz, Sereina Rutschmann, Michael T. Monaghan, Michel Sartori
Software Mentions: 5
Published: about 8 years ago
10.1186/s12862-015-0289-1
Higher speciation and lower extinction rates influence mammal diversity gradients in Asia
Cited by: 17
Author(s): Krishnapriya Tamma, Uma Ramakrishnan
Software Mentions: 4
Published: almost 10 years ago
10.1371/journal.pone.0178389
Insight into Central Asian flora from the Cenozoic Tianshan montane origin and radiation of Lagochilus (Lamiaceae)
Cited by: 8
Author(s): Mingli Zhang, Xiao-Qing Zeng, Stewart C. Sanderson, V. V. Byalt, Alexander P. Sukhorukov
Software Mentions: 3
Published: about 7 years ago
10.1186/s12862-020-01628-1
Mid-Cenozoic climate change, extinction, and faunal turnover in Madagascar, and their bearing on the evolution of lemurs
Cited by: 14
Author(s): Laurie R. Godfrey, Karen E. Samonds, Justin W. Baldwin, Michael R. Sutherland, Jason M. Kamilar, Kristen L. Allfisher
Software Mentions: 3
Published: about 4 years ago
10.1186/1741-7007-10-12
Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates
Cited by: 341
Author(s): Katrin Nyakatura, Olaf R. P. Bininda‐Emonds
Software Mentions: 2
Published: over 12 years ago
10.1186/s12862-014-0210-3
The strange case of East African annual fishes: aridification correlates with diversification for a savannah aquatic group?
Cited by: 47
Author(s): Alexander Dorn, Zuzana Musilová, Matthias Platzer, Kathrin Reichwald, Alessandro Cellerino
Software Mentions: 2
Published: about 10 years ago
10.1186/s12862-015-0432-z
Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions
Cited by: 14
Author(s): Sacha Laurent, Marc Robinson‐Rechavi, Nicolas Salamin
Software Mentions: 2
Published: about 9 years ago
10.1186/s12862-018-1277-z
Insights into the historical assembly of global dryland floras: the diversification of Zygophyllaceae
Cited by: 18
Author(s): Songjie Wu, Linjing Zhang, Lin Li, Sheng‐Xiang Yu, Zhiduan Chen, Wei Wang
Software Mentions: 2
Published: almost 6 years ago
10.1186/s12862-018-1210-5
Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods
Cited by: 16
Author(s): Sebastián Duchêne, David A. Duchêne, Jemma L. Geoghegan, Zoe A. Dyson, Jane Hawkey, Kathryn E. Holt
Software Mentions: 2
Published: over 6 years ago
10.1098/rsbl.2016.0273
Estimating shifts in diversification rates based on higher-level phylogenies
Cited by: 7
Author(s): Tanja Stadler, Smrckova Jana
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pcbi.1003913
Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models
Cited by: 56
Author(s): Veronika Bošková, Sebastian Bonhoeffer, Tanja Stadler
Software Mentions: 2
Published: almost 10 years ago
10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f
Insights into the Early Epidemic Spread of Ebola in Sierra Leone Provided by Viral Sequence Data
Cited by: 68
Author(s): Tanja Stadler, Denise Kühnert, David A. Rasmussen, Louis du Plessis
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0176384
No evidence for the radiation time lag model after whole genome duplications in Teleostei
Cited by: 11
Author(s): Sacha Laurent, Nicolas Salamin, Marc Robinson‐Rechavi
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0138697
Evolution of Asian Interior Arid-Zone Biota: Evidence from the Diversification of Asian Zygophyllum (Zygophyllaceae)
Cited by: 21
Author(s): Songjie Wu, Lin Li, Honglei Li, Sheng‐Xiang Yu, Linjing Zhang, Wei Wang
Software Mentions: 2
Published: about 9 years ago
10.1111/evo.13593
History is written by the victors: The effect of the push of the past on the fossil record
Cited by: 54
Author(s): Graham E. Budd, Richard P. Mann
Software Mentions: 2
Published: about 6 years ago
10.3389/fgene.2018.00698
Morphological Innovations and Vast Extensions of Mountain Habitats Triggered Rapid Diversification Within the Species-Rich Irano-Turanian Genus Acantholimon (Plumbaginaceae)
Cited by: 18
Author(s): Farideh Moharrek, Isabel Sanmartín, Shahrokh Kazempour Osaloo, Gonzalo Nieto Feliner
Software Mentions: 2
Published: almost 6 years ago
10.1038/srep19208
Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?
Cited by: 101
Author(s): Fabien L. Condamine, Matthew E. Clapham, Gaël J. Kergoat
Software Mentions: 2
Published: almost 9 years ago
10.1038/srep27259
The rise of angiosperm-dominated herbaceous floras: Insights from Ranunculaceae
Cited by: 40
Author(s): Wei Wang, Lin Li, Xiao‐Guo Xiang, Rosa Del C. Ortiz, Yang Liu, Kunli Xiang, Sheng‐Xiang Yu, Yao‐Wu Xing, Zhi Chen
Software Mentions: 1
Published: over 8 years ago
10.1186/s12862-015-0459-1
Range expansion and habitat shift triggered elevated diversification of the rice genus (Oryza, Poaceae) during the Pleistocene
Cited by: 2
Author(s): Lin Li, Liang Tang, Yunjun Bai, Zhiyao Tang, Wei Wang, Zhi Chen
Software Mentions: 1
Published: about 9 years ago
10.1186/1471-2148-14-118
The explosive radiation of Cheirolophus (Asteraceae, Cardueae) in Macaronesia
Cited by: 45
Author(s): Daniel Vitales, Teresa Garnatje, Jaume Pellicer, Joan Vallès, Arnoldo Santos‐Guerra, Isabel Sanmartín
Software Mentions: 1
Published: almost 11 years ago
10.3389/fgene.2016.00035
Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage
Cited by: 53
Author(s): Isabel Sanmartín, Andrea S. Meseguer
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pcbi.1007999
Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts
Cited by: 24
Author(s): Andrew F. Magee, Sebastian Höhna, Tetyana I. Vasylyeva, Adam D. Leaché, Vladimir N. Minin
Software Mentions: 1
Published: about 4 years ago
10.1098/rspb.2017.0095
Dry habitats were crucibles of domestication in the evolution of agriculture in ants
Cited by: 122
Author(s): Michael G. Branstetter, Ana Ješovnik, Jeffrey Sosa‐Calvo, Michael W. Lloyd, Brant C. Faircloth, Seán G. Brady, Ted R. Schultz
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0049521
Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix
Cited by: 460
Author(s): Mark S. Springer, Robert W. Meredith, John Gatesy, Christopher A. Emerling, Jong Hwan Park, Daniel L. Rabosky, Tanja Stadler, Cynthia Steiner, Oliver A. Ryder, Jan E. Janečka, Colleen A. Fisher, William J. Murphy
Software Mentions: 1
Published: almost 12 years ago
10.1038/srep16016
Mosaic patterns of diversification dynamics following the colonization of Melanesian islands
Cited by: 30
Author(s): Emmanuel F. A. Toussaint, Lars Hendrich, Helena Shaverdo, Michael Balke
Software Mentions: 1
Published: about 9 years ago
10.1186/s12862-014-0220-1
Cretaceous environmental changes led to high extinction rates in a hyperdiverse beetle family
Cited by: 48
Author(s): Gaël J. Kergoat, Patrice Bouchard, Anne Laure Clamens, Jessica Lee Abbate, Hervé Jourdan, Roula Jabbour‐Zahab, Guénaëlle Genson, Laurent Soldati, Fabien L. Condamine
Software Mentions: 1
Published: about 10 years ago