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: treedater

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

Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation
3 versions
Latest release: almost 5 years ago
157 downloads last month

Papers Mentioning treedater 16

10.1038/s42003-021-02025-0

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy
Cited by: 23
Author(s): Marta Giovanetti, Eleonora Cella, Francesca Benedetti, Brittany Rife Magalis, Vagner Fonseca, Silvia Fabris, Giovanni Campisi, Alessandra Ciccozzi, Silvia Angeletti, Alessândra Borsetti, Vittoradolfo Tambone, Caterina Sagnelli, Stefano Pascarella, Alberto Riva, Giancarlo Ceccarelli, Alessandro Marcello, Taj Azarian, Eduan Wilkinson, Túlio de Oliveira, Luiz Carlos Júnior Alcântara, Roberto Cauda, Arnaldo Caruso, Natalie E. Dean, Cameron J. Browne, José Lourenço, Marco Salemi, Davide Zella, Massimo Ciccozzi
Software Mentions: 17
Published: over 3 years ago

10.1002/cpz1.60

Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo
Cited by: 24
Author(s): Xavier Didelot, Michaela Kendall, Yuanwei Xu, Peter J White, Noel D. McCarthy
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.ppat.1008179

Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand
Cited by: 24
Author(s): Morgane Rolland, Sodsai Tovanabutra, Bethany L. Dearlove, Yifan Li, Christopher L. Owen, Éric Lewitus, Eric Sanders‐Buell, Meera Bose, Anne Marie O’Sullivan, Raabya Rossenkhan, Jan Phillipus Lourens Labuschagne, Paul T. Edlefsen, Daniel B. Reeves, Gustavo H. Kijak, Shana Miller, Kultida Poltavee, Jenica Lee, Lydia Bonar, Elizabeth A. Harbolick, Bahar Ahani, Phuc Pham, Hannah Kibuuka, Lucas Maganga, Sorachai Nitayaphan, Fred Sawe, Leigh Anne Eller, Robert A. Gramzinski, Jerome H. Kim, Nelson L. Michael, Merlin L. Robb
Software Mentions: 6
Published: almost 5 years ago

10.3389/fmicb.2021.655567

Molecular Evolution of Human Norovirus GII.2 Clusters
Cited by: 7
Author(s): Xingguang Li, Haizhou Liu, Brittany Rife Magalis, Sergei L. Kosakovsky Pond, Erik Volz
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-019-6007-4

Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses
Cited by: 30
Author(s): José Salvatore Leister Patané, Joaquim Martins, Luiz Thibério Rangel, José Belasque, Luciano Antônio Digiampietri, Agda Paula Facincani, Rafael Marini Ferreira, Fabrício José Jaciani, Yunzeng Zhang, Alessandro M. Varani, Nalvo F. Almeida, Nian Wang, Jesus Aparecido Ferro, Leandro Márcio Moreira, João Carlos Setúbal
Software Mentions: 4
Published: over 5 years ago

10.1093/molbev/msaa222

Log Transformation Improves Dating of Phylogenies
Cited by: 4
Author(s): Uyen Mai, Siavash Mirarab
Software Mentions: 4
Published: over 4 years ago

10.3390/v13010133

Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia
Cited by: 48
Author(s): Alix Armero, Nicolás Berthet, Jean‐Christophe Avarre
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1007046

A new method for inferring timetrees from temporally sampled molecular sequences
Cited by: 14
Author(s): Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar
Software Mentions: 3
Published: almost 5 years ago

10.1101/2021.01.18.427056

Model design for non-parametric phylodynamic inference and applications to pathogen surveillance
Cited by: 3
Author(s): Xavier Didelot, Lily Geidelberg, Erik Volz
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.cell.2020.11.020

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Cited by: 787
Author(s): Erik Volz, Verity Hill, John McCrone, Anna Price, David A. Jorgensen, Áine O’Toole, Joel Southgate, Robert A. Johnson, Ben Jackson, Fabrícia F. Nascimento, Sara Rey, Samuel M. Nicholls, Rachel Colquhoun, Ana da Silva Filipe, James G. Shepherd, David Pascall, Rajiv Shah, Natasha Jesudason, Kathy Li, Ruth F. Jarrett, Nicole Pacchiarini, Matthew Bull, Lily Geidelberg, Igor Siveroni, Ian Goodfellow, Nicholas J. Loman, Oliver G. Pybus, David L. Robertson, Emma C. Thomson, Andrew Rambaut, Thomas R. Connor
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pmed.1002961

High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain
Cited by: 50
Author(s): Yuanwei Xu, Irving Cancino-Muñoz, Manuela Torres-Puente, Luis M Villamayor, Rafael Borrás, María Borrás-Máñez, Montserrat Bosque, Juan J. Camarena, Ester Colomer-Roig, Javier Colomina, Isabel Escribano, Oscar Esparcia-Rodríguez, Ana Gil-Brusola, Concepción Gimeno, Adelina Gimeno-Gascón, Bárbara Gomila-Sard, Damiana González-Granda, Nieves Gonzalo-Jiménez, María Remedio Guna-Serrano, José Luís López-Hontangas, Coral Martín-González, Rosario Moreno-Muñoz, David Navarro, Marı́a Luisa Navarro, Nieves Orta, Elvira Pérez Pérez, Josep Morera Prat, Juan Carlos Rodrı́guez, María Montserrat Ruiz-García, Herme Vanaclocha, Caroline Colijn, Iñaki Comas
Software Mentions: 2
Published: about 5 years ago

10.1093/molbev/msaa193

Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies
Cited by: 26
Author(s): Xavier Didelot, Igor Siveroni, Erik Volz
Software Mentions: 2
Published: over 4 years ago

10.1093/ve/veaa102

Genomic epidemiology of a densely sampled COVID-19 outbreak in China
Cited by: 16
Author(s): Lily Geidelberg, Olivia Boyd, David A. Jorgensen, Igor Siveroni, Fabrícia F. Nascimento, Robert A. Johnson, Manon Ragonnet‐Cronin, Han Fu, Haowei Wang, Xiaoyue Xi, Wei Chen, Liu Dehui, Yingying Chen, Mengmeng Tian, Wenfeng Tan, Junjie Zai, Wanying Sun, Jiandong Li, Junhua Li, Erik Volz, Xingguang Li, Qing Nie
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.ppat.1007368

An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
Cited by: 19
Author(s): Pilar Domingo‐Calap, Benjamin Schubert, Mélanie Joly, Morgane Solis, Meiggie Untrau, Raphaël Carapito, Philippe Georgel, Sophie Caillard, Samira Fafi‐Kremer, Nicodème Paul, Oliver Kohlbacher, Fernando González‐Candelas, Seiamak Bahram
Software Mentions: 2
Published: about 6 years ago

10.1089/aid.2018.0039

HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men
Cited by: 25
Author(s): Ann M. Dennis, Erik Volz, Simon D. W. Frost, Mukarram Hossain, Art F. Y. Poon, Peter F Rebeiro, Sten H. Vermund, Timothy R. Sterling, Marcia L. Kalish
Software Mentions: 1
Published: about 6 years ago

10.1093/ve/veaa082

Emerging phylogenetic structure of the SARS-CoV-2 pandemic
Cited by: 21
Author(s): Nicholas M. Fountain-Jones, Raima Carol Appaw, Scott Carver, Xavier Didelot, Erik Volz, Michael A. Charleston
Software Mentions: 1
Published: over 4 years ago