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
10.12688/f1000research.17548.2
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and PythonCited by: 8
Author(s): Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Software Mentions: 13
Published: over 5 years ago
10.1099/mgen.0.000131
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing readsCited by: 370
Author(s): Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 12
Published: about 7 years ago
10.7554/eLife.60474
The effect of hybridization on transposable element accumulation in an undomesticated fungal speciesCited by: 26
Author(s): Mathieu Hénault, Souhir Marsit, Guillaume Charron, Christian R. Landry
Software Mentions: 12
Published: about 4 years ago
10.1002/aps3.11344
A basic dd <scp>RAD</scp> seq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four generaCited by: 20
Author(s): Ingrid E. Jordon‐Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels
Software Mentions: 9
Published: over 4 years ago
10.15252/msb.20198831
The impact of the genetic background on gene deletion phenotypes in <i>Saccharomyces cerevisiae</i>Cited by: 40
Author(s): Marco Galardini, Bede P. Busby, Cristina Viéitez, Alistair S. Dunham, Athanasios Typas, Pedro Beltrão
Software Mentions: 7
Published: almost 5 years ago
10.3389/fpls.2020.582422
Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental GeodynamicsCited by: 7
Author(s): Alan W. Meerow, Elliot M. Gardner, Kyoko Nakamura
Software Mentions: 7
Published: about 4 years ago
10.3390/jof7030226
The Destructive Tree Pathogen Phytophthora ramorum Originates from the Laurosilva Forests of East AsiaCited by: 34
Author(s): Thomas S. Jung, Marília Horta Jung, Joan Webber, Koji Kageyama, Ayaka Hieno, Hayato Masuya, Satoshi Uematsu, A. Pérez‐Sierra, Anna Harris, Jack Forster, Harvey Rees, Bruno Scanu, Sneha Patra, Tomáš Kudláček, Jan Janoušek, Tamara Corcobado, Ivan Milenković, Zoltán Á. Nagy, Ildikó Csorba, J. Bakonyi, C. M. Brasier
Software Mentions: 6
Published: over 3 years ago
10.1186/1471-2105-14-158
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenientCited by: 33
Author(s): Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena F. Deus, Brian L. Sidlauskas, Christian M. Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger A. Vos, Campbell O. Webb, Luke J. Harmon, Megan Pirrung, Brian C. O’Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenberg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane McTavish, Jeet Sukumaran, Mark W. Westneat, Michael E. Alfaro, Aaron Steele, G. Gulli Jordan
Software Mentions: 6
Published: over 11 years ago
10.1371/journal.pone.0148203
A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)Cited by: 67
Author(s): Simon Uribe‐Convers, Matthew L. Settles, David C. Tank
Software Mentions: 6
Published: almost 9 years ago
10.3389/fmicb.2020.591093
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency TestCited by: 8
Author(s): David Dylus, Trestan Pillonel, Onya Opota, Daniel Wüthrich, Helena M. B. Seth-Smith, Adrian Egli, Stefano Leo, Vladimir Lazarević, Jacques Schrenzel, Sacha Laurent, Claire Bertelli, Dominique Blanc, Stefan Neuenschwander, Alban Ramette, Laurent Falquet, Frank Imkamp, Peter M. Keller, André Kahles, Simone Oberhaensli, Valérie Barbié, Christophe Dessimoz, Gilbert Greub, Aitana Lebrand
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13029-015-0042-6
PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocolsCited by: 3
Author(s): Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A. Swertz
Software Mentions: 6
Published: about 9 years ago
10.1186/s40793-019-0342-6
The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisersCited by: 46
Author(s): Axel Aigle, James I. Prosser, Cécile Gubry‐Rangin
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pcbi.1004842
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample SizesCited by: 522
Author(s): Jerome Kelleher, Alison Etheridge, Gil McVean
Software Mentions: 5
Published: over 8 years ago
10.1093/gigascience/giy081
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolutionCited by: 14
Author(s): Xia Li, Dongmei Ai, Hojoon Lee, Noemi Andor, Chao Li, Nancy R. Zhang, Hanlee P. Ji
Software Mentions: 4
Published: over 6 years ago
10.1002/ece3.2961
Longevity is associated with relative brain size in birdsCited by: 46
Author(s): Piotr Minias, Patrycja Podlaszczuk
Software Mentions: 4
Published: over 7 years ago
10.1186/1471-2105-13-209
Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in BiopythonCited by: 116
Author(s): Eric Talevich, Brandon M. Invergo, Peter J. A. Cock, Brad Chapman
Software Mentions: 4
Published: over 12 years ago
10.7717/peerj.3569
Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?Cited by: 42
Author(s): Malvina Kadlec, Baoheng Du, Nicholas C Le Maitre, Michael D. Pirie
Software Mentions: 4
Published: over 7 years ago
10.1038/s41598-020-68497-y
Species traits predict the aryl hydrocarbon receptor 1 (AHR1) subtypes responsible for dioxin sensitivity in birdsCited by: 5
Author(s): Kristin Bianchini, Christy A. Morrissey
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0139047
Pyvolve: A Flexible Python Module for Simulating Sequences along PhylogeniesCited by: 83
Author(s): Scott R. Spielman, Claus O. Wilke
Software Mentions: 4
Published: about 9 years ago
10.1371/journal.pcbi.1008924
Incorporating the speciation process into species delimitationCited by: 48
Author(s): Jeet Sukumaran, Mark T. Holder, L. Lacey Knowles
Software Mentions: 4
Published: over 3 years ago
10.1186/1471-2105-12-63
BIO::Phylo-phyloinformatic analysis using perlCited by: 44
Author(s): Rutger A. Vos, Jason Caravas, Klaas Hartmann, Mark A. Jensen, Chase Miller
Software Mentions: 4
Published: over 13 years ago
10.3389/fpubh.2020.00455
Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in Modern Mycobacterium tuberculosis LineagesCited by: 1
Author(s): Alexander C. Outhred, Ulziijargal Gurjav, Peter Jelfs, Nadine McCallum, Qinning Wang, Grant A. Hill-Cawthorne, Ben J. Marais, Vitali Sintchenko
Software Mentions: 4
Published: about 4 years ago
10.1186/s13071-019-3656-8
Predicting West Nile virus transmission in North American bird communities using phylogenetic mixed effects models and eBird citizen science dataCited by: 21
Author(s): Morgan P. Kain, Benjamin M. Bolker
Software Mentions: 4
Published: over 5 years ago
10.1093/sysbio/syv082
<i>SimPhy</i>: Phylogenomic Simulation of Gene, Locus, and Species TreesCited by: 116
Author(s): Diego Mallo, Leonardo de Oliveira Martins, David Posada
Software Mentions: 3
Published: about 9 years ago
10.1002/ece3.6714
The relationship between morphology and behavior in mixed‐species flocks of island birdsCited by: 4
Author(s): Brian C. Weeks, Shahid Naeem, Benjamin M. Winger, Joel Cracraft
Software Mentions: 3
Published: about 4 years ago
10.1002/ece3.7429
Rivers, not refugia, drove diversification in arboreal, sub‐Saharan African snakesCited by: 10
Author(s): Kaitlin E. Allen, Eli Greenbaum, Paul M Hime, Walter Paulin Tapondjou N., Viktoria V. Sterkhova, Chifundera Kusamba, Mark‐Oliver Rödel, Johannes Penner, A. Townsend Peterson, Rafe M. Brown
Software Mentions: 3
Published: over 3 years ago
10.1016/j.dib.2016.01.069
Data supporting phylogenetic reconstructions of the Neotropical clade GymnotiformesCited by: 6
Author(s): Victor Alberto Tagliacollo, Maxwell J. Bernt, Jack M. Craig, Cláudio Oliveira, James S. Albert
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pcbi.1004186
Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature WeightingCited by: 24
Author(s): Davide Albanese, Carlotta De Filippo, Duccio Cavalieri, Claudio Donati
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pcbi.1008561
Sampling bias and model choice in continuous phylogeography: Getting lost on a random walkCited by: 40
Author(s): Antanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stéphane Guindon, Nicola De Maio
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pntd.0007930
Genetic diversity of laboratory strains and implications for research: The case of Aedes aegyptiCited by: 31
Author(s): Andrea Gloria‐Soria, John Soghigian, David Kellner, Jeffrey R. Powell
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pone.0080589
Phylogenetic Relatedness of Circulating HIV-1C Variants in Mochudi, BotswanaCited by: 31
Author(s): Vladimir Novitsky, Hermann Bussmann, Andrew Logan, Sikhulile Moyo, Erik van Widenfelt, Lillian Okui, Mompati Mmalane, Jeannie Baca, Linda B. Buck, Eleanor Phillips, David Todem, Mary Fran McLane, Quanhong Lei, Rui Wang, Joseph Makhema, Shahin Lockman, Victor DeGruttola, Max Essex
Software Mentions: 3
Published: almost 11 years ago
10.1186/s12862-017-1066-0
Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)Cited by: 51
Author(s): Jessica A. Goodheart, Adam L. Bazinet, Ángel Valdés, Allen G. Collins, Michael P. Cummings
Software Mentions: 3
Published: about 7 years ago
10.1038/s41598-019-52613-8
Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methodsCited by: 2
Author(s): Kimia Kamelian, Vincent Montoya, Andrea D. Olmstead, Winnie Dong, Richard Harrigan, Muhammad Morshed, Jeffrey B. Joy
Software Mentions: 3
Published: about 5 years ago
10.1038/s41598-017-17794-0
Anatomical evidence for scent guided foraging in the turkey vultureCited by: 34
Author(s): Nathan P. Grigg, Justin M. Krilow, Cristian Gutiérrez-Ibáñez, Douglas R. Wylie, Gary R. Graves, Andrew N. Iwaniuk
Software Mentions: 3
Published: almost 7 years ago
10.1186/s43008-020-00051-x
Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)Cited by: 5
Author(s): Felix Grewe, Claudio Gennaro Ametrano, Todd J. Widhelm, Steven D. Leavitt, Isabel Distefano, Wetchasart Polyiam, David Pizarro, Mats Wedin, Ana Crespo, Pradeep K. Divakar, H. Thorsten Lumbsch
Software Mentions: 3
Published: almost 4 years ago
10.1093/molbev/msaa100
Structural Phylogenetics with ConfidenceCited by: 5
Author(s): Ashar J Malik, Anthony M. Poole, Jane R. Allison
Software Mentions: 3
Published: over 4 years ago
10.1093/molbev/msx273
Spatial and Temporal Scales of Range Expansion in Wild Phaseolus vulgarisCited by: 48
Author(s): Andrea Ariani, Jorge C. Berny Mier y Teran, Paul Gepts
Software Mentions: 3
Published: about 7 years ago
10.1093/gbe/evt195
Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered PastCited by: 21
Author(s): Robert Eveleigh, Conor J. Meehan, John M. Archibald, Robert G. Beiko
Software Mentions: 3
Published: almost 11 years ago
10.3390/genes9090456
Functional Evolution of Avian RIG-I-Like ReceptorsCited by: 12
Author(s): Wanjing Zheng, Yoko Satta
Software Mentions: 3
Published: about 6 years ago
10.3389/fmicb.2017.00456
Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic ResistanceCited by: 30
Author(s): Juan Castro‐Severyn, Francisco Remonsellez, Sandro L. Valenzuela, Cesar Salinas, Jonathan Fortt, Pablo S. Aguilar, Coral Pardo-Esté, Cristina Dorador, Raquel Quatrini, Franck Molina, Daniel Aguayo, Eduardo Castro-Nallar, Claudia P. Saavedra
Software Mentions: 3
Published: over 7 years ago
10.7554/eLife.05503
Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovationCited by: 140
Author(s): Christopher E. Laumer, Andreas Hejnol, Gonzalo Giribet
Software Mentions: 2
Published: over 9 years ago
10.1186/s12859-020-03750-9
AllCoPol: inferring allele co-ancestry in polyploidsCited by: 12
Author(s): Ulrich Lautenschlager, Florian Wagner, Christoph Oberprieler
Software Mentions: 2
Published: about 4 years ago
10.1186/1471-2105-14-330
Agalma: an automated phylogenomics workflowCited by: 132
Author(s): Casey W. Dunn, Mark Howison, Felipe Zapata
Software Mentions: 2
Published: about 11 years ago
10.1186/s12859-021-04274-6
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of LifeCited by: 1
Author(s): Luna L. Sánchez‐Reyes, Martha Kandziora, Emily Jane McTavish
Software Mentions: 2
Published: over 3 years ago
10.1186/s12915-017-0397-z
Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paraloguesCited by: 93
Author(s): Rohan Bythell-Douglas, Carl J. Rothfels, Dennis Stevenson, Sean W. Graham, Gane Ka‐Shu Wong, David C. Nelson, Tom Bennett
Software Mentions: 2
Published: over 7 years ago
10.1186/1471-2148-12-57
Molecular phylogeny of grunts (Teleostei, Haemulidae), with an emphasis on the ecology, evolution, and speciation history of New World speciesCited by: 45
Author(s): José Tavera, Arturo Acero P., Eduardo F. Balart, Giacomo Bernardi
Software Mentions: 2
Published: almost 13 years ago
10.1186/1471-2148-12-171
Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus dataCited by: 78
Author(s): Ryan P. Lamers, Gowrishankar Muthukrishnan, Todd A. Castoe, Sergio Tafur, Alexander M. Cole, Christopher L. Parkinson
Software Mentions: 2
Published: about 12 years ago
10.1186/1471-2148-13-221
Looking for trees in the forest: summary tree from posterior samplesCited by: 123
Author(s): Joseph Heled, Remco Bouckaert
Software Mentions: 2
Published: almost 12 years ago
10.1186/s12862-020-01644-1
One species, two developmental modes: a case of geographic poecilogony in marine gastropodsCited by: 9
Author(s): Benedikt Wiggering, Marco T. Neiber, Katharina Gebauer, Matthias Glaubrecht
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-016-3101-8
Scaling statistical multiple sequence alignment to large datasetsCited by: 13
Author(s): Michael Nute, Tandy Warnow
Software Mentions: 2
Published: about 8 years ago
10.1093/bioinformatics/bty474
BioStructMap: a Python tool for integration of protein structure and sequence-based featuresCited by: 9
Author(s): Andrew Guy, Vashti Irani, Jack S. Richards, Paul A. Ramsland
Software Mentions: 2
Published: over 6 years ago
10.3390/microorganisms9010191
Core and Accessory Genome Analysis of Vibrio mimicusCited by: 5
Author(s): Iliana Guardiola-Avila, Leonor Sánchez-Busó, Evelia Acedo-Félix, Bruno Gómez‐Gil, Manuel Zúñiga, Fernando Gónzález-Candelas, Lorena Noriega-Orozco
Software Mentions: 2
Published: almost 4 years ago
10.1080/23802359.2018.1522982
Complete mitogenome of the biocontroller fungus Purpureocillium sp. (Ascomycota, Ophiocordycipitaceae, Hypocreales)Cited by: 2
Author(s): Nadya Lorena Cardona, Nicolás D. Franco‐Sierra, Javier Correa Álvarez
Software Mentions: 2
Published: over 6 years ago
10.7717/peerj.340
The evolutionary history and diagnostic utility of the CRISPR-Cas system within<i>Salmonella enterica</i>ssp.<i>enterica</i>Cited by: 30
Author(s): James B. Pettengill, Ruth Timme, Rodolphe Barrangou, Mauricio Toro, Marc W. Allard, Errol Strain, Steven M. Musser, Eric W. Brown
Software Mentions: 2
Published: over 10 years ago
10.7717/peerj.187
PhyBin: binning trees by topologyCited by: 13
Author(s): Ryan Newton, Irene L. G. Newton
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pcbi.1002567
ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein OriginCited by: 79
Author(s): John A. Capra, Ann B. Williams, Katherine S. Pollard
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0173235
Avian binocular vision: It’s not just about what birds can see, it’s also about what they can’tCited by: 18
Author(s): Luke P. Tyrrell, Esteban Fernández‐Juricic
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0082615
Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory StudyCited by: 89
Author(s): Adam L. Bazinet, Michael P. Cummings, Kim T. Mitter, Charles Mitter
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0241178
Identification of plastid genomic regions inferring species identity from de novo plastid genome assembly of 14 Korean-native Iris species (Iridaceae)Cited by: 9
Author(s): Yang Jae Kang, Soonok Kim, Jung-Ho Lee, Hyosig Won, Gi-Heum Nam, Myounghai Kwak
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0113872
The Evolutionary Fate of the Horizontally Transferred Agrobacterial Mikimopine Synthase Gene in the Genera Nicotiana and LinariaCited by: 17
Author(s): Viera Kováčová, Jitka Žlůvová, Bohuslav Janoušek, Martina Talianová, Boris Vyskot
Software Mentions: 2
Published: almost 10 years ago
10.1002/ece3.4888
A journey on plate tectonics sheds light on European crayfish phylogeographyCited by: 20
Author(s): Lucian Pârvulescu, Jorge L. Pérez‐Moreno, Cristian Panaiotu, Lucian Drăguţ, Anne Schrimpf, Ioana‐Diana Popovici, Claudia Zaharia, András Weiperth, Blanka Gál, Christoph D. Schubart, Heather D. Bracken‐Grissom
Software Mentions: 2
Published: almost 6 years ago
10.3389/fpls.2020.584981
The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome DataCited by: 5
Author(s): Ran Meng, Liying Luo, Jiyuan Zhang, Dai-Gui Zhang, Ze‐Long Nie, Ying Meng
Software Mentions: 2
Published: almost 4 years ago
10.1186/s13073-015-0176-9
Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic dataCited by: 39
Author(s): Jason W. Sahl, James M. Schupp, David A. Rasko, Rebecca E. Colman, Jeffrey T. Foster, Paul Keim
Software Mentions: 2
Published: over 9 years ago
10.1098/rsos.150196
Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigationCited by: 44
Author(s): Jessica A. Goodheart, Adam L. Bazinet, Allen G. Collins, Michael P. Cummings
Software Mentions: 2
Published: about 9 years ago
10.1038/s41598-018-33806-z
Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species ActCited by: 47
Author(s): Nathan A. Johnson, Chase H. Smith, John M. Pfeiffer, Charles R. Randklev, James D. Williams, James D. Austin
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-019-45455-x
Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota)Cited by: 32
Author(s): Todd J. Widhelm, Felix Grewe, Jen‐Pan Huang, Joel A. Mercado‐Díaz, Bernard Goffinet, Robert Lücking, Bibiana Moncada, Roberta J. Mason‐Gamer, H. Thorsten Lumbsch
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-021-88323-3
New species and a new record of Phylloporia from BeninCited by: 1
Author(s): Boris Armel Olou, Nourou S. Yorou, Ewald Langer
Software Mentions: 2
Published: over 3 years ago
10.1093/sysbio/syv118
Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other MethodsCited by: 105
Author(s): Huw A. Ogilvie, Joseph Heled, Donghua Xie, Alexei J. Drummond
Software Mentions: 2
Published: almost 9 years ago
10.1128/mBio.00846-16
The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic MarkersCited by: 45
Author(s): Jason W. Sahl, Adam J. Vazquez, Carina M. Hall, Joseph D. Busch, Apichai Tuanyok, Mark Mayo, James M. Schupp, Madeline Lummis, Talima Pearson, Kenzie Shippy, Rebecca E. Colman, Christopher John Allender, Vanessa Theobald, Derek S. Sarovich, Erin P. Price, Alex Hutcheson, Jonas Korlach, John J. LiPuma, Jason T. Ladner, Sean Lovett, G. I. Koroleva, Gustavo Palacios, Direk Limmathurotsakul, Vanaporn Wuthiekanun, Gumphol Wongsuwan, Bart J. Currie, Paul Keim, David M. Wagner
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0071069
The Rediscovery of a Long Described Species Reveals Additional Complexity in Speciation Patterns of Poeciliid Fishes in Sulfide SpringsCited by: 46
Author(s): Maura Palacios Mejia, Lenin Arias‐Rodríguez, Martin Plath, Constanze Eifert, Hannes Lerp, Anton Lamboj, Gary Voelker, Michael Tobler
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0021885
Species Interactions during Diversification and Community Assembly in an Island Radiation of ShrewsCited by: 30
Author(s): Jacob A. Esselstyn, Sean P. Maher, Rafe M. Brown
Software Mentions: 1
Published: over 13 years ago
10.1093/sysbio/syx090
Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided ProposalsCited by: 28
Author(s): Mathieu Fourment, Brian C. Claywell, Vu Dinh, Connor O. McCoy, F. A. Matsen, Aaron E. Darling
Software Mentions: 1
Published: almost 7 years ago
10.1093/sysbio/syy006
Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian IsthmusCited by: 115
Author(s): Madlen Stange, Marcelo R. Sánchez‐Villagra, Walter Salzburger, Michael Matschiner
Software Mentions: 1
Published: almost 7 years ago
10.1016/j.dib.2017.05.024
Data on the time of integration of the human mitochondrial pseudogenes (NUMTs) into the nuclear genomeCited by: 3
Author(s): Konstantin Gunbin, Leonid Peshkin, Konstantin Popadin, Sofia Annis, Rebecca Rogers Ackermann, Konstantin Khrapko
Software Mentions: 1
Published: over 7 years ago
10.3897/phytokeys.50.4940
The resurrection of Neohattoria Kamim. (Jubulaceae, Marchantiophyta): a six decade systematic conflict resolved through a molecular perspectiveCited by: 11
Author(s): Juan Larraín, Ben Carter, Blanka Shaw, Jörn Hentschel, Lynika Strozier, Tatsuwo Furuki, Jochen Heinrichs, Barbara Crandall‐Stotler, John J. Engel, Matt Von Konrat
Software Mentions: 1
Published: over 9 years ago
10.1093/database/baz022
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolutionCited by: 8
Author(s): Kevin Correia, Shi Miao Yu, Radhakrishnan Mahadevan
Software Mentions: 1
Published: almost 6 years ago
10.7717/peerj.7531
Molecular taxonomy of endemic coastal <i>Ligia</i> isopods from the Hawaiian Islands: re-description of <i>L. hawaiensis</i> and description of seven novel cryptic speciesCited by: 8
Author(s): Carlos Santamaría
Software Mentions: 1
Published: over 5 years ago
10.1002/ece3.2397
Multiple transisthmian divergences, extensive cryptic diversity, occasional long‐distance dispersal, and biogeographic patterns in a marine coastal isopod with an amphi‐American distributionCited by: 22
Author(s): Luis A. Hurtado, Mariana Mateos, Gustavo Mattos, Shuang Liu, Pilar A. Haye, Paulo Cesar Paiva
Software Mentions: 1
Published: about 8 years ago
10.1186/1471-2148-12-177
Limited, episodic diversification and contrasting phylogeography in a New Zealand cicada radiationCited by: 24
Author(s): David C. Marshall, Kathy B. R. Hill, Katharine A. Marske, Colleen Chambers, Thomas R. Buckley, Chris Simon
Software Mentions: 1
Published: almost 13 years ago
10.7717/peerj.4658
Molecular approaches uncover cryptic diversity in intertidal<i>Ligia</i>isopods (Crustacea, Isopoda, Ligiidae) across the southern Africa coastlineCited by: 14
Author(s): Taylor M Greenan, Charles L. Griffiths, Carlos Santamaría
Software Mentions: 1
Published: over 6 years ago
10.7717/peerj.6180
The origin of exotic pet sugar gliders (<i>Petaurus breviceps</i>) kept in the United States of AmericaCited by: 8
Author(s): Catriona D. Campbell, Jill Pecon-Slattery, Rebecca M Pollak, Leo Joseph, Clare E. Holleley
Software Mentions: 1
Published: almost 6 years ago
10.1002/ece3.2599
Phylogeographic patterns of a lower intertidal isopod in the Gulf of California and the Caribbean and comparison with other intertidal isopodsCited by: 10
Author(s): Luis A. Hurtado, Mariana Mateos, Shuang Liu
Software Mentions: 1
Published: almost 8 years ago
10.7717/peerj.6142
Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virusCited by: 3
Author(s): Therese A. Catanach, Andrew D. Sweet, Nam Nguyen, Rhiannon Peery, Andrew H. Debevec, Andrea K. Thomer, Amanda C. Owings, Bret M. Boyd, Aron D. Katz, Felipe N. Soto-Adames, Julie M. Allen
Software Mentions: 1
Published: almost 6 years ago
10.7717/peerj.3894
Cryptic biodiversity and phylogeographic patterns of Seychellois<i>Ligia</i>isopodsCited by: 10
Author(s): Carlos Santamaría, Joanna K. Bluemel, Nancy Bunbury, Melinda Curran
Software Mentions: 1
Published: about 7 years ago
10.7717/peerj.2968
Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islandsCited by: 55
Author(s): Mauricio Diazgranados, Janet C. Barber
Software Mentions: 1
Published: almost 8 years ago
10.7717/peerj.4337
Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod<i>Ligia exotica</i>Cited by: 6
Author(s): Luis A. Hurtado, Mariana Mateos, Chang Wang, Carlos Santamaría, Jongwoo Jung, Valiallah Khalaji-Pirbalouty, Won Kim
Software Mentions: 1
Published: over 6 years ago
10.1186/s12862-017-1020-1
Pan-genome and phylogeny of Bacillus cereus sensu latoCited by: 78
Author(s): Adam L. Bazinet
Software Mentions: 1
Published: over 7 years ago
10.3389/fpls.2021.667060
The Complete Chloroplast Genome of Plukenetia volubilis Provides Insights Into the Organelle InheritanceCited by: 4
Author(s): Simón Villanueva-Corrales, Camilo García-Botero, Froilán Garcés-Cardona, Viviana Ramírez-Ríos, Diego F. Villanueva-Mejía, Javier Correa Álvarez
Software Mentions: 1
Published: over 3 years ago
10.3897/zookeys.517.9308
Scleractinian corals (Fungiidae, Agariciidae and Euphylliidae) of Pulau Layang-Layang, Spratly Islands, with a note on Pavona maldivensis (Gardiner, 1905)Cited by: 19
Author(s): Zarinah Waheed, Francesca Benzoni, Sancia E. T. van der Meij, Tullia Isotta Terraneo, Bert W. Hoeksema
Software Mentions: 1
Published: over 9 years ago
10.1093/ve/vew016
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic casesCited by: 108
Author(s): Armando Arias, Simon J. Watson, Danny Asogun, Ekaete Alice Tobin, Lianshun Jia, My Phan, Umaru Jah, Raoul Emeric Guetiya Wadoum, Luke Meredith, Lucy Thorne, Sarah Caddy, Alimamy Tarawalie, Pinky Langat, Gytis Dudas, Nuno Rodrigues Faria, Simon Dellicour, Abdul Kamara, Brima Kargbo, Brima Osaio Kamara, Sahr Sm Gevao, Daniel J. Cooper, Matthew Newport, Peter Horby, Jake Dunning, Foday Sahr, Tim Brooks, Andrew J. H. Simpson, Elisabetta Groppelli, Guoying Li, Nisha Mulakken, Kate Rhodes, James Akpablie, Zabulon Yoti, Margaret Lamunu, Esther Vitto, Patrick Otim, Collins Owilli, Isaac Boateng, Lawrence Ehis Okoror, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Ighodalo Yemisis, Donatus I Adomeh, Solomon Ehikhiametalor, Patience Akhilomen, Chris Aire, Andreas Kurth, Nicola Cook, Jan Baumann, Marcin Gabriel, Roman Wölfel, Antonino Di, Miles W. Carroll, Stephan Günther, John T. Redd, Dhamari Naidoo, Oliver G. Pybus, Andrew Rambaut, Paul Kellam, Ian Goodfellow, Matthew Cotten
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12985-015-0286-4
Sequencing and phylogenetic analysis of the gp51 gene from Korean bovine leukemia virus isolatesCited by: 28
Author(s): Eunjung Lee, Eunju Kim, Ha-Kyung Joung, Bo-Hye Kim, Jae‐Young Song, In‐Soo Cho, Kyoung-Ki Lee, Yeun-Kyung Shin
Software Mentions: 1
Published: over 9 years ago
10.3897/mycokeys.65.47574
Diversity of Trametes (Polyporales, Basidiomycota) in tropical Benin and description of new species Trametes parvisporaCited by: 3
Author(s): Boris Armel Olou, Franz‐Sebastian Krah, Meike Piepenbring, Nourou S. Yorou, Ewald Langer
Software Mentions: 1
Published: over 4 years ago
10.1093/gbe/evz191
Balancing Selection Drives the Maintenance of Genetic Variation in Drosophila Antimicrobial PeptidesCited by: 34
Author(s): J. R. Chapman, Tom Hill, Robert L. Unckless
Software Mentions: 1
Published: about 5 years ago
10.1186/s12859-016-1303-3
MEvoLib v1.0: the first molecular evolution library for PythonCited by: 1
Author(s): Jorge Álvarez-Jarreta, Eduardo Ruiz‐Pesini
Software Mentions: 1
Published: about 8 years ago
10.1093/biomet/asx047
Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic treesCited by: 32
Author(s): Tom M. W. Nye, Xiaoxian Tang, Grady Weyenberg, Ruriko Yoshida
Software Mentions: 1
Published: about 7 years ago
10.1186/s12864-015-1663-5
Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preferenceCited by: 20
Author(s): Joy Scaria, Haruo Suzuki, Christopher Ptak, Jenn Wei Chen, Yongzhang Zhu, Xiaokui Guo, Yung Fu Chang
Software Mentions: 1
Published: over 9 years ago
10.1098/rsos.140375
Rapid diversification and secondary sympatry in Australo-Pacific kingfishers (Aves: Alcedinidae:<i>Todiramphus</i>)Cited by: 61
Author(s): Michael J. Andersen, Hannah T. Shult, Alice Cibois, Jean‐Claude Thibault, Christopher E. Filardi, Robert G. Moyle
Software Mentions: 1
Published: almost 10 years ago
10.1186/1471-2148-14-132
EM for phylogenetic topology reconstruction on nonhomogeneous dataCited by: 0
Author(s): Esther Ibáñez‐Marcelo, Marta Casanellas
Software Mentions: 1
Published: almost 11 years ago
10.1038/srep17345
Exploring molecular variation in Schistosoma japonicum in ChinaCited by: 26
Author(s): Neil D. Young, Kok‐Gan Chan, Pasi K. Korhonen, Teik Min Chong, Robson Ee, Namitha Mohandas, Anson V. Koehler, Yan-Lue Lim, Andreas Hofmann, Aaron R. Jex, Qian Bao-zhen, Neil B. Chilton, Geoffrey N. Gobert, Donald P. McManus, Patrick Tan, Bonnie L. Webster, David Rollinson, Robin B. Gasser
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12864-018-4621-1
SIESTA: enhancing searches for optimal supertrees and species treesCited by: 3
Author(s): Pranjal Vachaspati, Tandy Warnow
Software Mentions: 1
Published: over 6 years ago