pypi: DendroPy | Projects | Ecosyste.ms: Papers

10.12688/f1000research.17548.2

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Cited 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 reads
Cited 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 species
Cited 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 genera
Cited 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 Saccharomyces cerevisiae
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 Geodynamics
Cited 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 Asia
Cited 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 convenient
Cited 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 Test
Cited 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: about 4 years ago

10.1186/s13029-015-0042-6

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols
Cited 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-oxidisers
Cited 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 Sizes
Cited 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 evolution
Cited 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 birds
Cited 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 Biopython
Cited 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 birds
Cited 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 Phylogenies
Cited 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 delimitation
Cited 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 perl
Cited 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 Lineages
Cited 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 data
Cited by: 21
Author(s): Morgan P. Kain, Benjamin M. Bolker
Software Mentions: 4
Published: over 5 years ago

10.1093/sysbio/syv082

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees
Cited 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 birds
Cited 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 snakes
Cited 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 Gymnotiformes
Cited 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 Weighting
Cited 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 walk
Cited 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 aegypti
Cited 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, Botswana
Cited 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 methods
Cited 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 vulture
Cited 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 Confidence
Cited 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 vulgaris
Cited 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 Past
Cited 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 Receptors
Cited 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 Resistance
Cited 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 innovation
Cited 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 polyploids
Cited 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 workflow
Cited 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 Life
Cited 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 paralogues
Cited 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 species
Cited 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 data
Cited 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 samples
Cited 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 gastropods
Cited 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 datasets
Cited 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 features
Cited 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 mimicus
Cited 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 withinSalmonella entericassp.enterica
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 topology
Cited 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 Origin
Cited 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’t
Cited 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 Study
Cited 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 Linaria
Cited by: 17
Author(s): Viera Kováčová, Jitka Žlůvová, Bohuslav Janoušek, Martina Talianová, Boris Vyskot
Software Mentions: 2
Published: about 10 years ago

10.1002/ece3.4888

A journey on plate tectonics sheds light on European crayfish phylogeography
Cited 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 Data
Cited 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 data
Cited 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 investigation
Cited 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 Act
Cited 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 Benin
Cited 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 Methods
Cited 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 Markers
Cited 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 Springs
Cited 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 Shrews
Cited 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 Proposals
Cited 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 Isthmus
Cited 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 genome
Cited 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 perspective
Cited 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 evolution
Cited 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 Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species
Cited 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 distribution
Cited 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 radiation
Cited 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 intertidalLigiaisopods (Crustacea, Isopoda, Ligiidae) across the southern Africa coastline
Cited 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 (Petaurus breviceps) kept in the United States of America
Cited 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 isopods
Cited 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 virus
Cited 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 SeychelloisLigiaisopods
Cited 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 islands
Cited 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 isopodLigia exotica
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 lato
Cited 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 Inheritance
Cited 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 cases
Cited 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 isolates
Cited 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 parvispora
Cited 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 Peptides
Cited 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 Python
Cited 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 trees
Cited 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 preference
Cited 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:Todiramphus)
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 data
Cited 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 China
Cited 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 trees
Cited by: 3
Author(s): Pranjal Vachaspati, Tandy Warnow
Software Mentions: 1
Published: over 6 years ago

Projects: pypi: DendroPy

Papers Mentioning DendroPy 119