UPGMA


Also found in: Wikipedia.
AcronymDefinition
UPGMAUnweighted Pair Group Method with Averages (microbiology)
UPGMAUnweighted Pair Group Mean Average
UPGMAUnweighted Pair Group Method of Analysis (microbiology)
UPGMAUnweighted Pair Group Method of Association (microbiology)
UPGMAUnweighted Pair Group Method, Arithmetic Mean
References in periodicals archive ?
In addition, UPGMA trees were inferred from K2P distances with MEGA 5.
Considering allelic richness, allele frequencies, and the UPGMA phenogram, we suggest that the populations CF1 and CF-7 from one of the clusters and CF-5 and CF-6 from the other cluster deserve both in situ preservation and ex situ conservation in southern Korea.
Our results show that pelagic shark species display distinct thermal niche partitioning (as identified by UPGMA clustering) and that habitat structure for the epipelagic silky and oceanic whitetip sharks can be adequately estimated from two dimensions (these species spend most of their time in the warmest available water).
UPGMA clustering analyses almost completely separated American lines from those of Indian lines.
O agrupamento hierarquico UPGMA (Figura 1) obteve maior valor para a correlacao cofenetica (CCC = 0,80) que aqueles verificados para os metodos de agrupamento, utilizando-se Ward (0,50) e o Vizinho Mais Proximo (0,60).
4] Nonstandard abbreviations: PFGE, pulsed-field gel electrophoresis; DLA, direct linear analysis; NARSA, Network on Antimicrobial Resistance in Staphylococcus aureus; MAH, Mount Auburn Hospital; A, absorbance; UPGMA, unweighted pair group method with arithmetic mean; SSI, sample similarity index; PFT, pulsed-field type; MLST, multilocus sequence type.
Population genetic structure was tested by constructing an UPGMA phenogram to portray genetic relationships among individuals using the software package PAUP 4.
Allocation of archaeological stones to extant morphological groups defined by UPGMA Archaeological Site Cultural period context N Morphotype AM Persian period 2 III Egyptian Roman period MMS3 11 III (n = 3) Egyptian (n = 5) unclassified (n = 3) MMS6 1 unclassified MMS19 9 III (n = 4) Egyptian (n = 4) unclassified (n = 1) MMS23 5 I1I (n = 2) Egyptian (n = 1) unclassified (n = 2) MMS47 2 III unclassified MMS51 4 Egyptian (n = 1) unclassified (n = 3) MMS61 8 III (n = 1) Egyptian (n = 4) unclassified (n = 3) MMS523 2 Egyptian unclassified MQ 3 Egyptian (n = 2) unclassified Z Roman period 8 Egyptian (n = 4) III-IV-V (n = 2) unclassified (n = 2) Probability of Site N allocation AM 2 0.
Using the UPGMA routine in PHYLIP, we completed one analysis of all 129 fragments and one analysis of just the 53 that occurred twice.
The average linkage between groups method is a commonly used method for forming clusters and is referred to simply as UPGMA.
Trees were constructed from these distances with the NEIGHBOR and FITCH programs to create neighbor-joining (Saitou and Nei 1987), and UPGMA (Sokal and Michener 1958) trees.
There are a number of hierarchical analysis methods including neighbour joining and UPGMA clustering to help identify groups of samples within the dataset.