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: pypi: DendroPy

https://packages.ecosyste.ms/registries/pypi.org/packages/DendroPy

A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
24 versions
Latest release: over 1 year ago
24 dependent packages
5,103 downloads last month

Papers Mentioning DendroPy 119

10.1038/s41598-018-22592-3

Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures
Cited by: 18
Author(s): Andrew Guy, Vashti Irani, James G. Beeson, Benjamin Webb, Andrej Šali, Jack S. Richards, Paul A. Ramsland
Software Mentions: 1
Published: over 6 years ago

10.1099/vir.0.000071

Discovery of a polyomavirus in European badgers (Meles meles) and the evolution of host range in the family Polyomaviridae
Cited by: 12
Author(s): Sarah C. Hill, Aisling A. Murphy, Matthew Cotten, Anne L. Palser, Phillip Benson, Sandrine Lesellier, Eamonn Gormley, Céline Richomme, Sylvia S. Grierson, Deirdre Ní Bhuachalla, Mark A. Chambers, Paul Kellam, María-Laura Boschiroli, Bernhard Ehlers, Michael A. Jarvis, Oliver G. Pybus
Software Mentions: 1
Published: over 9 years ago

10.1155/2012/780169

Phylogeographic Diversity of the Lower Central American Cichlid<i>Andinoacara coeruleopunctatus</i>(Cichlidae)
Cited by: 7
Author(s): S. Shawn McCafferty, Andrew P. Martin, Eldredge Bermingham
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-13-38

Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae
Cited by: 55
Author(s): Haruo Suzuki, Tristan Lefébure, Paulina Pavinski Bitar, Michael J. Stanhope
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-020-66761-9

Identification and characterization of Colletotrichum species causing apple bitter rot in New York and description of C. noveboracense sp. nov.
Cited by: 44
Author(s): Fatemeh Khodadadi, Jonathan González, Phillip L. Martin, Emily Giroux, Guillaume J. Bilodeau, Kari A. Peter, Vinson P. Doyle, Srđan G. Aćimović
Software Mentions: 1
Published: about 4 years ago

10.1186/s12862-016-0786-x

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye
Cited by: 76
Author(s): Richard Harrington, Brant C. Faircloth, Ron I. Eytan, W. W. Smíth, Thomas J. Near, Michael E. Alfaro, Matt Friedman
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0148949

A Global Population Genetic Study of Pantala flavescens
Cited by: 74
Author(s): Daniel Troast, Frank Suhling, Hiroshi Jinguji, Göran Sahlén, Jessica L. Ware
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0224599

Phylogenetic revision of Gymnotidae (Teleostei: Gymnotiformes), with descriptions of six subgenera
Cited by: 8
Author(s): Jack M. Craig, Lesley Y. Kim, Victor Alberto Tagliacollo, James S. Albert
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0085103

Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer
Cited by: 12
Author(s): Nicholas J. Matzke, Patrick M. Shih, Cheryl A. Kerfeld
Software Mentions: 1
Published: over 10 years ago

10.7554/eLife.01339

tRNA genes rapidly change in evolution to meet novel translational demands
Cited by: 80
Author(s): Avihu H. Yona, Zohar Bloom-Ackermann, Idan Frumkin, Victor Hanson-Smith, Yoav Charpak-Amikam, Qinghua Feng, Jef D. Boeke, Orna Dahan, Yitzhak Pilpel
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0067827

Contrasting Phylogeography of Sandy vs. Rocky Supralittoral Isopods in the Megadiverse and Geologically Dynamic Gulf of California and Adjacent Areas
Cited by: 30
Author(s): Luis A. Hurtado, Eun Jung Lee, Mariana Mateos
Software Mentions: 1
Published: about 11 years ago

10.1371/currents.outbreaks.c7fd7946ba606c982668a96bcba43c90

High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants
Cited by: 22
Author(s): Kevin Emmett, Albert Lee, Hossein Khiabanian, Raúl Rabadán
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0094081

Global Diversification at the Harsh Sea-Land Interface: Mitochondrial Phylogeny of the Supralittoral Isopod Genus Tylos (Tylidae, Oniscidea)
Cited by: 18
Author(s): Luis A. Hurtado, Mi Kyung Lee, Mariana Mateos, Stefano Taiti
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0085199

A Complex Evolutionary History in a Remote Archipelago: Phylogeography and Morphometrics of the Hawaiian Endemic Ligia Isopods
Cited by: 25
Author(s): Carlos Santamaría, Mariana Mateos, Stefano Taiti, Azhari Azhari, Luis A. Hurtado
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0221631

Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction
Cited by: 3
Author(s): D. Gamermann, Arnau Montagud, J. Alberto Conejero, Pedro Fernández de Córdoba, Javier F. Urchueguı́a
Software Mentions: 1
Published: about 5 years ago

10.1186/s12862-017-1002-3

Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini)
Cited by: 48
Author(s): Hermes E. Escalona, Andreas Zwick, Hao‐Sen Li, Jiahui Li, Xingmin Wang, Diana Hartley, Lars S. Jermiin, Oldřich Nedvěd, Bernhard Misof, Oliver Niehuis, Adam Ślipinśki, Wioletta Tomaszewska
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0136296

Phylogeny of Acronychia (Rutaceae) and First Insights into Its Historical Biogeography and the Evolution of Fruit Characters
Cited by: 6
Author(s): Laura Holzmeyer, Marco F. Duretto, Darren M. Crayn, Elvira Hörandl, Margaret M. Heslewood, Janani Jayanthan, Marc S. Appelhans
Software Mentions: 1
Published: about 9 years ago

10.3390/plants9111497

Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae)
Cited by: 6
Author(s): Caiyun Zhang, Tong-Jian Liu, Xiaolu Mo, Hui-Run Huang, Gang Yao, Jiànróng Lǐ, Xue‐Jun Ge, Hai‐Fei Yan
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0065226

Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections
Cited by: 182
Author(s): Stephen J. Salipante, Dhruba J. SenGupta, Christopher Rosenthal, Gina L. Costa, Jessica Spangler, Elizabeth H. Sims, Michael A. Jacobs, Samuel I. Miller, Daniel R. Hoogestraat, Brad T. Cookson, Connor O. McCoy, F. A. Matsen, Jay Shendure, Clarence C. Lee, Timothy T. Harkins, Noah G. Hoffman
Software Mentions: 1
Published: over 11 years ago