Stochastic Safety Radius on UPGMA [PDF]
Algorithms, 2022 Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree from a distance matrix computed from an alignment of sequences.
Ruriko Yoshida +2 more
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UPGMA - analysis of type II CRISPR RNA-guided endonuclease Cas9 homologues from the compost metagenome [PDF]
E3S Web of Conferences, 2021 Metagenomic approaches provide access to the genetic diversity of the environment for biotechnological applications, allowing the discovery of new enzymes and new pathways for numerous catalytic processes.
Zimin Andrei A. +2 more
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Nonunique UPGMA clusterings of microsatellite markers [PDF]
Briefings in Bioinformatics, 2022 Abstract Agglomerative hierarchical clustering has become a common tool for the analysis and visualization of data, thus being present in a large amount of scientific research and predating all areas of bioinformatics and computational biology.
Segura-Alabart, Natàlia +3 more
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Multiple UPGMA and Neighbor-joining Trees and the Performance of Some Computer Packages [PDF]
Molecular Biology and Evolution, 1996 *Royal Belgian Institute of Natural Sciences, Brussels; and TDepartments of Biology and SBiochemistry, University of Antwerp Although the unweighted pair-group method using arithmetic averages (UPGMA) and neighbor-joining (NJ) algo- rithms are designed to produce single trees, they may derive more than one topology from a single matrix, depending on ...
Backeljau, Thierry +5 more
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MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL [PDF]
Evolutionary Bioinformatics, 2017 A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic ...
Guan-Jie Hua +5 more
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Polyhedral combinatorics of UPGMA cones [PDF]
Advances in Applied Mathematics, 2013 Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive orthant induced by classifying the input vectors according to tree topologies returned by the algorithm.
Davidson, Ruth, Sullivant, Seth
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UPGMA and the normalized equidistant minimum evolution problem [PDF]
Theoretical Computer Science, 2018 29 pages, 8 ...
Vincent Moulton +2 more
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UPGMA and artificial neural networks applications on wild type olives
Journal of Environmental Biology, 2017 Scientific Research Projects Coordination Unit of Manisa Celal Bayer University, Manisa ...
Oglu, E. D. Yegen +3 more
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THE GENOMIC-DNA RELATIONSHIP OF SOME WILD ACCESSIONS OF COWPEA (VIGNASPP) USING UN-WEIGHTED PAIR GROUP METHOD OF ARITHMETIC MEANS (UPGMA) [PDF]
Acta Scientifica MalaysiaThe Genomic-DNA of five wild accessions (TVnu-59, TVnu-561, TVnu-563, TVnu-1148 and TVnu-1395) of Cowpea (Vigna species) using Un-weighted Pair Group Method of Arithmetic Means (UPGMA) was carried out at African Bioscience Laboratory, Ibadan, Oyo State ...
V.J. Adavbiele +2 more
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A Comparative Analysis of Progressive Multiple Sequence Alignment Approaches using UPGMA and Neighbor Join Based Guide Trees [PDF]
International Journal of Computer Science, Engineering and Information Technology, 2015 Multiple sequence alignment is increasingly important to bioinformatics, with several applications ranging from phylogenetic analyses to domain identification. There are several ways to perform multiple sequence alignment, an important way of which is the progressive alignment approach studied in this work.
Dega, Ravi Kumar Yadav, Ercal, Gunes
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