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: tidytree
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/tidytree
A Tidy Tool for Phylogenetic Tree Data Manipulation
29 versions
Latest release: over 1 year ago
6 dependent packages
25,296 downloads last month
Papers Mentioning tidytree 10
10.1038/s42003-021-02025-0
SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in ItalyCited 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
10.1534/g3.120.401612
A Reference Genome Sequence for Giant SequoiaCited by: 53
Author(s): Alison Dawn Scott, Aleksey V. Zimin, Daniela Puiu, Rachael E. Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily E. Burns, Jill L. Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Software Mentions: 11
Published: about 4 years ago
10.3390/plants8120547
New Insights on Lilium Phylogeny Based on a Comparative Phylogenomic Study Using Complete Plastome SequencesCited by: 12
Author(s): Hyoung Tae Kim, Ki-Byung Lim, Jung Sung Kim
Software Mentions: 11
Published: almost 5 years ago
10.1128/mSphere.00743-20
Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull ( <i>Chroicocephalus novaehollandiae</i> ) Reveals the Acquisition of Multidrug Resistance PlasmidsCited by: 17
Author(s): Max L. Cummins, Martina L. Sanderson-Smith, Peter Newton, Nicholas Carlile, David N. Phalen, Kimberly Maute, Leigh G. Monahan, Bethany J. Hoye, Steven P. Djordjevic
Software Mentions: 10
Published: almost 4 years ago
10.1073/pnas.2104254118
Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolutionCited by: 22
Author(s): Nicolas Blavet, Hua Yang, Handong Su, Pavel Solanský, Ryan N. Douglas, Miroslava Karafiátová, Lucie Šimková, Jing Zhang, Yalin Liu, Jie Hou, Xiaowen Shi, Chen Chen, Mohamed El-Walid, Morgan McCaw, Patrice S. Albert, Zhi Gao, Changzeng Zhao, Gil Ben-Zvi, Lior Glick, Guy Kol, Jinghua Shi, Jan Vrána, Hana Šimková, Jonathan C. Lamb, Kathleen J. Newton, R. Kelly Dawe, Jaroslav Doležel, Tieming Ji, Kobi Baruch, Fangpu Han, James A. Birchler, Jan Bartoš
Software Mentions: 9
Published: over 3 years ago
10.1111/2041-210X.13422
nosoi: A stochastic agent‐based transmission chain simulation framework in <scp>r</scp>Cited by: 19
Author(s): Sébastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele
Software Mentions: 8
Published: over 4 years ago
10.1093/molbev/msab166
ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic DataCited by: 101
Author(s): Shuaimei Xu, Zhigang Dai, Pingfan Guo, Xiaocong Fu, Shanshan Liu, Lang Zhou, Wenli Tang, Tingze Feng, Meijun Chen, Li Zhan, Tianzhi Wu, Erqiang Hu, Yong Jiang, Xiaochen Bo, Guangchuang Yu
Software Mentions: 8
Published: over 3 years ago
10.1128/mSphere.00056-20
Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North AmericaCited by: 19
Author(s): Elizabeth A. Miller, Ehud Elnekave, Cristian Flores-Figueroa, Abigail Johnson, Ashley Kearney, Jeannette Muñoz-Aguayo, Kaitlin A. Tagg, Lorelee Tschetter, Bonnie Weber, Céline Nadon, Dave Boxrud, Randall S. Singer, Jason P. Folster, Timothy J. Johnson
Software Mentions: 7
Published: over 4 years ago
10.3389/fmicb.2019.01108
A Systematic Approach to Identify and Characterize the Effectiveness and Safety of Novel Probiotic Strains to Control Foodborne PathogensCited by: 35
Author(s): Diana Ayala, Peter W. Cook, Jorge G. Franco, Marie Bugarel, Kameswara Rao Kottapalli, Guy H. Loneragan, Mindy M. Brashears, Kendra K. Nightingale
Software Mentions: 6
Published: over 5 years ago
10.1093/molbev/msab081
A Comprehensive Phylogenetic Analysis of the Serpin SuperfamilyCited by: 32
Author(s): Matthew A. Spence, Matthew D. Mortimer, Ashley M. Buckle, Bùi Quang Minh, C.J. Jackson
Software Mentions: 5
Published: over 3 years ago