Journal articles on the topic 'Phylogenomic trees'
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Lee, Michael D. "Applications and Considerations of GToTree: A User-Friendly Workflow for Phylogenomics." Evolutionary Bioinformatics 15 (January 2019): 117693431986224. http://dx.doi.org/10.1177/1176934319862245.
Full textAy, Hilal, Hayrettin Saygin, and Nevzat Sahin. "Phylogenomic revision of the family Streptosporangiaceae, reclassification of Desertactinospora gelatinilytica as Spongiactinospora gelatinilytica comb. nov. and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae." International Journal of Systematic and Evolutionary Microbiology 70, no. 4 (April 1, 2020): 2569–79. http://dx.doi.org/10.1099/ijsem.0.004073.
Full textCheon, Seongmin, Jianzhi Zhang, and Chungoo Park. "Is Phylotranscriptomics as Reliable as Phylogenomics?" Molecular Biology and Evolution 37, no. 12 (July 13, 2020): 3672–83. http://dx.doi.org/10.1093/molbev/msaa181.
Full textGaltier, Nicolas, and Vincent Daubin. "Dealing with incongruence in phylogenomic analyses." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1512 (October 7, 2008): 4023–29. http://dx.doi.org/10.1098/rstb.2008.0144.
Full textShah, Toral, Fandey H. Mashimba, Haji O. Suleiman, Yahya S. Mbailwa, Julio V. Schneider, Georg Zizka, Vincent Savolainen, Isabel Larridon, and Iain Darbyshire. "Phylogenetics of Ochna (Ochnaceae) and a new infrageneric classification." Botanical Journal of the Linnean Society 198, no. 4 (December 3, 2021): 361–81. http://dx.doi.org/10.1093/botlinnean/boab071.
Full textVinh, Lê Sỹ. "Phylogenetic and Phylogenomic Analyses for Large Datasets." Journal of Research and Development on Information and Communication Technology 2019, no. 2 (December 31, 2019): 84–92. http://dx.doi.org/10.32913/mic-ict-research.v2019.n2.898.
Full textXiao, Guohua, Guirong Tang, and Chengshu Wang. "Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi." Journal of Fungi 6, no. 3 (August 13, 2020): 134. http://dx.doi.org/10.3390/jof6030134.
Full textJiang, Xiaodong, Scott V. Edwards, and Liang Liu. "The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets." Systematic Biology 69, no. 4 (February 3, 2020): 795–812. http://dx.doi.org/10.1093/sysbio/syaa008.
Full textLee, Michael D. "GToTree: a user-friendly workflow for phylogenomics." Bioinformatics 35, no. 20 (March 13, 2019): 4162–64. http://dx.doi.org/10.1093/bioinformatics/btz188.
Full textZhang, Chao, Celine Scornavacca, Erin K. Molloy, and Siavash Mirarab. "ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy." Molecular Biology and Evolution 37, no. 11 (September 4, 2020): 3292–307. http://dx.doi.org/10.1093/molbev/msaa139.
Full textLiu, Liang, Shaoyuan Wu, and Lili Yu. "Coalescent methods for estimating species trees from phylogenomic data." Journal of Systematics and Evolution 53, no. 5 (June 19, 2015): 380–90. http://dx.doi.org/10.1111/jse.12160.
Full textMallo, Diego, Leonardo De Oliveira Martins, and David Posada. "SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees." Systematic Biology 65, no. 2 (November 1, 2015): 334–44. http://dx.doi.org/10.1093/sysbio/syv082.
Full textScornavacca, C., V. Berry, and V. Ranwez. "Building species trees from larger parts of phylogenomic databases." Information and Computation 209, no. 3 (March 2011): 590–605. http://dx.doi.org/10.1016/j.ic.2010.11.022.
Full textJennings, W. Bryan. "On the independent gene trees assumption in phylogenomic studies." Molecular Ecology 26, no. 19 (September 14, 2017): 4862–71. http://dx.doi.org/10.1111/mec.14274.
Full textVinh, Le Sy. "MODELING AMINO ACID SUBSTITUTIONS FOR WHOLE GENOMES." Journal of Computer Science and Cybernetics 37, no. 4 (October 12, 2021): 351–63. http://dx.doi.org/10.15625/1813-9663/37/4/15937.
Full textMinh, Bui Quang, Matthew W. Hahn, and Robert Lanfear. "New Methods to Calculate Concordance Factors for Phylogenomic Datasets." Molecular Biology and Evolution 37, no. 9 (May 4, 2020): 2727–33. http://dx.doi.org/10.1093/molbev/msaa106.
Full textWang, Yaxuan, Zhen Cao, Huw A. Ogilvie, and Luay Nakhleh. "Phylogenomic assessment of the role of hybridization and introgression in trait evolution." PLOS Genetics 17, no. 8 (August 18, 2021): e1009701. http://dx.doi.org/10.1371/journal.pgen.1009701.
Full textKimball, Rebecca T., Carl H. Oliveros, Ning Wang, Noor D. White, F. Keith Barker, Daniel J. Field, Daniel T. Ksepka, et al. "A Phylogenomic Supertree of Birds." Diversity 11, no. 7 (July 10, 2019): 109. http://dx.doi.org/10.3390/d11070109.
Full textPaule, Juraj, Roswitha Schmickl, Tomáš Fér, Sabine Matuszak-Renger, Heidemarie Halbritter, and Georg Zizka. "Phylogenomic insights into the Fascicularia-Ochagavia group (Bromelioideae, Bromeliaceae)." Botanical Journal of the Linnean Society 192, no. 4 (December 21, 2019): 642–55. http://dx.doi.org/10.1093/botlinnean/boz085.
Full textChernomor, Olga, Bui Quang Minh, and Arndt von Haeseler. "Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference." Journal of Computational Biology 22, no. 12 (December 2015): 1129–42. http://dx.doi.org/10.1089/cmb.2015.0146.
Full textJ. Page, Andrew, Martin Hunt, Torsten Seemann, and Jacqueline A. Keane. "SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs." Journal of Open Source Software 2, no. 13 (May 3, 2017): 243. http://dx.doi.org/10.21105/joss.00243.
Full textSteenwyk, Jacob L., Thomas J. Buida, Abigail L. Labella, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. "PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data." Bioinformatics 37, no. 16 (February 9, 2021): 2325–31. http://dx.doi.org/10.1093/bioinformatics/btab096.
Full textSaarela, Jeffery M., Sean V. Burke, William P. Wysocki, Matthew D. Barrett, Lynn G. Clark, Joseph M. Craine, Paul M. Peterson, Robert J. Soreng, Maria S. Vorontsova, and Melvin R. Duvall. "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions." PeerJ 6 (February 2, 2018): e4299. http://dx.doi.org/10.7717/peerj.4299.
Full textMcGowen, Michael R., Georgia Tsagkogeorga, Sandra Álvarez-Carretero, Mario dos Reis, Monika Struebig, Robert Deaville, Paul D. Jepson, et al. "Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture." Systematic Biology 69, no. 3 (October 21, 2019): 479–501. http://dx.doi.org/10.1093/sysbio/syz068.
Full textMai, Uyen, and Siavash Mirarab. "Completing gene trees without species trees in sub-quadratic time." Bioinformatics 38, no. 6 (January 3, 2022): 1532–41. http://dx.doi.org/10.1093/bioinformatics/btab875.
Full textTimme, Ruth E., Hugh Rand, Martin Shumway, Eija K. Trees, Mustafa Simmons, Richa Agarwala, Steven Davis, et al. "Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance." PeerJ 5 (October 6, 2017): e3893. http://dx.doi.org/10.7717/peerj.3893.
Full textZhou, Xiaofan, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz Von Looz, and Antonis Rokas. "Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence." Systematic Biology 69, no. 2 (August 29, 2019): 308–24. http://dx.doi.org/10.1093/sysbio/syz058.
Full textStephens, Timothy G., Debashish Bhattacharya, Mark A. Ragan, and Cheong Xin Chan. "PhySortR: a fast, flexible tool for sorting phylogenetic trees in R." PeerJ 4 (May 12, 2016): e2038. http://dx.doi.org/10.7717/peerj.2038.
Full textBordenstein, S. R., C. Paraskevopoulos, J. C. Dunning Hotopp, P. Sapountzis, N. Lo, C. Bandi, H. Tettelin, J. H. Werren, and K. Bourtzis. "Parasitism and Mutualism in Wolbachia: What the Phylogenomic Trees Can and Cannot Say." Molecular Biology and Evolution 26, no. 1 (October 6, 2008): 231–41. http://dx.doi.org/10.1093/molbev/msn243.
Full textAllio, Rémi, Céline Scornavacca, Benoit Nabholz, Anne-Laure Clamens, Felix AH Sperling, and Fabien L. Condamine. "Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution." Systematic Biology 69, no. 1 (May 7, 2019): 38–60. http://dx.doi.org/10.1093/sysbio/syz030.
Full textDorrell, Richard G., Adrien Villain, Benoît Perez-Lamarque, Guillemette Audren de Kerdrel, Giselle McCallum, Andrew K. Watson, Ouardia Ait-Mohamed, et al. "Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes." Proceedings of the National Academy of Sciences 118, no. 4 (January 8, 2021): e2009974118. http://dx.doi.org/10.1073/pnas.2009974118.
Full textDorrell, Richard G., Adrien Villain, Benoît Perez-Lamarque, Guillemette Audren de Kerdrel, Giselle McCallum, Andrew K. Watson, Ouardia Ait-Mohamed, et al. "Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes." Proceedings of the National Academy of Sciences 118, no. 4 (January 8, 2021): e2009974118. http://dx.doi.org/10.1073/pnas.2009974118.
Full textSmith, Brian Tilston, William M. Mauck, Brett W. Benz, and Michael J. Andersen. "Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets." Genome Biology and Evolution 12, no. 7 (May 29, 2020): 1131–47. http://dx.doi.org/10.1093/gbe/evaa113.
Full textWainaina, James M., Elijah Ateka, Timothy Makori, Monica A. Kehoe, and Laura M. Boykin. "Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya." PeerJ 6 (July 19, 2018): e5254. http://dx.doi.org/10.7717/peerj.5254.
Full textNelson, Thomas C., Angela M. Stathos, Daniel D. Vanderpool, Findley R. Finseth, Yao-wu Yuan, and Lila Fishman. "Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)." PLOS Genetics 17, no. 2 (February 22, 2021): e1009095. http://dx.doi.org/10.1371/journal.pgen.1009095.
Full textRabiee, Maryam, and Siavash Mirarab. "INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores." Systematic Biology 69, no. 2 (August 12, 2019): 384–91. http://dx.doi.org/10.1093/sysbio/syz045.
Full textShen, Xing-Xing, Jacob L. Steenwyk, and Antonis Rokas. "Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data." Systematic Biology 70, no. 5 (February 22, 2021): 997–1014. http://dx.doi.org/10.1093/sysbio/syab011.
Full textBoeckmann, B., M. Robinson-Rechavi, I. Xenarios, and C. Dessimoz. "Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees." Briefings in Bioinformatics 12, no. 5 (July 7, 2011): 423–35. http://dx.doi.org/10.1093/bib/bbr034.
Full textSmith, Stephen A., Nathanael Walker-Hale, Joseph F. Walker, and Joseph W. Brown. "Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants." Systematic Biology 69, no. 3 (November 20, 2019): 579–92. http://dx.doi.org/10.1093/sysbio/syz078.
Full textChuang, Chia-Rong, Chia-Lun Hsieh, Chi-Shan Chang, Chiu-Mei Wang, Danilo N. Tandang, Elliot M. Gardner, Lauren Audi, Nyree J. C. Zerega, and Kuo-Fang Chung. "Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop—Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan." PLOS ONE 17, no. 9 (September 30, 2022): e0272680. http://dx.doi.org/10.1371/journal.pone.0272680.
Full textSteenwyk, Jacob L., Dayna C. Goltz, Thomas J. Buida, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. "OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees." PLOS Biology 20, no. 10 (October 13, 2022): e3001827. http://dx.doi.org/10.1371/journal.pbio.3001827.
Full textMiller, Justin B., Lauren M. McKinnon, Michael F. Whiting, and Perry G. Ridge. "CAM: an alignment-free method to recover phylogenies using codon aversion motifs." PeerJ 7 (June 4, 2019): e6984. http://dx.doi.org/10.7717/peerj.6984.
Full textGulyaev, Sergey, Xin-Jie Cai, Fei-Yi Guo, Satoshi Kikuchi, Wendy L. Applequist, Zhi-Xiang Zhang, Elvira Hörandl, and Li He. "The phylogeny of Salix revealed by whole genome re-sequencing suggests different sex-determination systems in major groups of the genus." Annals of Botany 129, no. 4 (March 23, 2022): 485–98. http://dx.doi.org/10.1093/aob/mcac012.
Full textSuh, Alexander. "The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves." Zoologica Scripta 45, S1 (September 27, 2016): 50–62. http://dx.doi.org/10.1111/zsc.12213.
Full textKarin, Benjamin R., Tony Gamble, and Todd R. Jackman. "Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements." Molecular Biology and Evolution 37, no. 3 (November 9, 2019): 904–22. http://dx.doi.org/10.1093/molbev/msz263.
Full textCerón-Romero, Mario A., Xyrus X. Maurer-Alcalá, Jean-David Grattepanche, Ying Yan, Miguel M. Fonseca, and L. A. Katz. "PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes." Molecular Biology and Evolution 36, no. 8 (May 7, 2019): 1831–42. http://dx.doi.org/10.1093/molbev/msz103.
Full textHeckenhauer, Jacqueline, Ovidiu Paun, Mark W. Chase, Peter S. Ashton, A. S. Kamariah, and Rosabelle Samuel. "Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes." Annals of Botany 123, no. 5 (December 12, 2018): 857–65. http://dx.doi.org/10.1093/aob/mcy220.
Full textJames, Timothy Y., Jason E. Stajich, Chris Todd Hittinger, and Antonis Rokas. "Toward a Fully Resolved Fungal Tree of Life." Annual Review of Microbiology 74, no. 1 (September 8, 2020): 291–313. http://dx.doi.org/10.1146/annurev-micro-022020-051835.
Full textStull, Gregory W., Pamela S. Soltis, Douglas E. Soltis, Matthew A. Gitzendanner, and Stephen A. Smith. "Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages." American Journal of Botany 107, no. 5 (May 2020): 790–805. http://dx.doi.org/10.1002/ajb2.1468.
Full textYoshida, Ruriko, Lillian Paul, and Peter Nesbitt. "Stochastic Safety Radius on UPGMA." Algorithms 15, no. 12 (December 18, 2022): 483. http://dx.doi.org/10.3390/a15120483.
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