Results 21 to 30 of about 23,568,791 (272)

Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment [PDF]

, 2005
The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes.
C Lemieux, CR Woese, CR Woese, D Sankoff, DH Moreira, E Chatton, E Mayr, E Pennisi, F Tekaia, FitchWM, GI McFadden, GI McFadden, GW Stuart, GW Stuart, J Adachi, J Las Rivas De, J Lin, J Qi, J Qi, J.Q. Deng, JA Eisen, JD Palmer, JR Brown, K.H. Chu, KH Chu, L.Q. Zhou, M Li, M Turmel, M Turmel, MA Ragan, MW Gray, MW Gray, N Saitou, O Weiss, RF Doolittle, RF Doolittle, RL Charlebois, RS Gupta, S.C. Long, ST Fitz-Gibbon, SV Edwards, V.V. Anh, VL Stirewalt, W Martin, W Martin, W Martin, Z.G. Yu, ZG Yu, ZG Yu, ZG Yu, ZG Yu   +50 more
core   +3 more sources

rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection. [PDF]

, 2013
Phylogenetic recombination detection is a fundamental task in bioinformatics and evolutionary biology. Most of the computational tools developed to attack this important problem are not integrated into the growing suite of R packages for statistical ...
Chattopadhyay, Sujay, Irvahn, Jan, Minin, Vladimir N, Sokurenko, Evgeni V   +3 more
core   +3 more sources

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

Science, 2020
Phylogenetics of superspreading One important characteristic of coronavirus epidemiology is the occurrence of superspreading events. These are marked by a disproportionate number of cases originating from often-times asymptomatic individuals.
J. Lemieux, K. Siddle, Bennett M. Shaw, C. Loreth, S. Schaffner, A. Gladden-Young, Gordon C Adams, Timelia Fink, C. Tomkins-Tinch, L. Krasilnikova, K. DeRuff, Melissa Rudy, Matthew R. Bauer, K. A. Lagerborg, Erica Normandin, S. Chapman, Steven K. Reilly, Melis N. Anahtar, Aaron E. Lin, Amber Carter, C. Myhrvold, Molly E Kemball, Sushma Chaluvadi, C. Cusick, Katelyn Flowers, A. Neumann, Felecia Cerrato, M. Farhat, D. Slater, J. Harris, J. Branda, D. Hooper, Jessie M. Gaeta, Travis P. Baggett, J. O'Connell, A. Gnirke, Tami D. Lieberman, A. Philippakis, Meagan Burns, Catherine M. Brown, J. Luban, E. Ryan, S. Turbett, R. Larocque, W. Hanage, G. Gallagher, L. Madoff, S. Smole, Virginia M. Pierce, E. Rosenberg, Pardis C Sabeti, Daniel J. Park, B. MacInnis   +52 more
semanticscholar   +1 more source

Past and future of a century old Citrus tristeza virus collection: a California citrus germplasm tale. [PDF]

, 2013
Citrus tristeza virus (CTV) isolates collected from citrus germplasm, dooryard and field trees in California from 1914 have been maintained in planta under quarantine in the Citrus Clonal Protection Program (CCPP), Riverside, California. This collection,
Georgios eVidalakis, Greg eGreer, James eDiaz, Jinbo eWang, Jinbo eWang, John eBash, Orhan eBozan, Ramon eSerna, Raymond K. Yokomi, Richard F Lee, Robert R Krueger, Sun-Jung eKwon, Svetlana Y Folimonova, Tavia eRucker, Tyler eDang   +14 more
core   +2 more sources

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

bioRxiv, 2023
Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of ...
L. Revell
semanticscholar   +1 more source

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

bioRxiv, 2020
Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org.
Benoit Morel, P. Barbera, Lucas Czech, Ben Bettisworth, Lukas Hübner, S. Lutteropp, Dora Serdari, E. Kostaki, I. Mamais, Alexey M. Kozlov, P. Pavlidis, D. Paraskevis, A. Stamatakis   +12 more
semanticscholar   +1 more source

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

Nucleic Acids Res., 2008
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree.
Alexis Dereeper, V. Guignon, Guillaume Blanc, S. Audic, S. Buffet, F. Chevenet, Jean-François Dufayard, Stéphane Guindon, Vincent Lefort, Magali Lescot, Jean-Michel Claverie, Olivier Gascuel   +11 more
semanticscholar   +1 more source

Choreography of silk spinning by webspinners (Insecta: Embioptera) reflects lifestyle and hints at phylogeny [PDF]

, 2016
Silk spinning defines the morphologically constrained embiopterans. All individuals spin for protection, including immatures, adult males and the wingless females. Enlarged front tarsi are packed with silk glands and clothed with ejectors.
Edgerly-Rooks, Janice, Hohu, Kyle, McMillan, David   +2 more
core   +2 more sources

Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis [PDF]

, 2012
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is distance-based, that
Daskalakis, Constantinos, Roch, Sebastien   +1 more
core   +2 more sources

Phylogenetic network analysis of SARS-CoV-2 genomes

Proceedings of the National Academy of Sciences of the United States of America, 2020
Significance This is a phylogenetic network of SARS-CoV-2 genomes sampled from across the world. These genomes are closely related and under evolutionary selection in their human hosts, sometimes with parallel evolution events, that is, the same virus ...
P. Forster, Lucy Forster, C. Renfrew, M. Forster   +3 more
semanticscholar   +1 more source