The genetic diversity study has paramount importance in breeding programs; hence, it allows selection and choice of the parental genetic divergence, which have the agronomic traits desired by the breeder. This study aimed to characterize the genetic divergence between 24 soybean genotypes through their agronomic traits, using multivariate clustering methods to select the potential genitors for ...

In examining genetic data in recent publications, Backeljau et al. showed cases in which two or more different trees (tie trees) were constructed from a single data set for the neighbor-joining (NJ) method and the unweighted pair group method with arithmetic mean (UPGMA). However, it is still unclear how often and under what conditions tie trees are generated. Therefore, I examined these proble...

The relative merits of four different tree-making methods in obtaining the correct topology were studied by using computer simulation. The methods studied were the unweighted pair-group method with arithmetic mean (UPGMA), Fitch and Margoliash's (FM) method, thd distance Wagner (DW) method, and Tateno et al.'s modified Farris (MF) method. An ancestral DNA sequence was assumed to evolve into eig...

In this paper, we present a hybrid clustering method that combines the divisive hierarchical clustering with the agglomerative hierarchical clustering. We used the bisect K-means divisive clustering algorithm in our method. First, we cluster the document collection using bisect K-means clustering algorithm with K’ > K as the total number of clusters. Second, we calculate the centroids of K’ clu...

This study was conducted to estimate genetic distances among Akkaraman, Morkaraman, Awassi, Merino, Karakul, Kivircik, Imroz, Daglic and Karayaka sheep breeds reared in Turkey based on simple polymorphic blood protein types by using various methods including horizontal strach gel electrophoresis and polyacrilamyde gel electrophoresis (PAGE). NJ and UPGMA trees were constructed based on genetic ...

We will use a variation of UPGMA in UPGMA we have a distance matrix, in each iteration we take the pair i, j with the minimal distance: ∀k, l : di,j < dk,l and create a new node which is their parent.In the UPGMA algorithm the new distances for this node is the average of the two distances of it’s children : ∀l : Di+j,l = 12 (di,l + dj,l). We will talk about a very similar idea for clustering g...

Department of Computer Science, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu City 30013, Taiwan Department of Computer Science and Information Engineering, Chang Gung University, No. 259, Sanmin Rd., Guishan Township, Taoyuan City 33302, Taiwan Department of Computer Science and Communication Engineering, Providence University, No. 200, Sec. 7, Taiwan Boulevard, Sha...

Terminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacter...

The bootstrapping method of determining confidence in the topology of phylogenetic trees has been applied to electrophoretic protein data for two groups of amphibians: salamanders of two North American genera (Aneides and Plethodon) of the tribe Plethodontini and Holarctic hylid frogs. Some current methods of phylogenetic reconstruction for electrophoretic protein data have been evaluated by co...