We have analysed the efficiency of all mitochondrial protein coding genes and six nuclear markers (Adora3, Adrb2, Bdnf, Irbp, Rag2 and Vwf) in reconstructing and statistically supporting known amniote groups (murines, rodents, primates, eutherians, metatherians, therians). The efficiencies of maximum likelihood, Bayesian inference, maximum parsimony, neighbor-joining and UPGMA were also evaluat...

Objectives. We aimed to explore the impact of gut microbiota in coronary heart disease (CHD) patients through high-throughput sequencing. Methods. A total of 29 CHD in-hospital patients and 35 healthy volunteers as controls were included. Nucleic acids were extracted from fecal samples, followed by α diversity and principal coordinate analysis (PCoA). Based on unweighted UniFrac distance matric...

UPGMA analysis, principal component analysis, genetic diversity analysis and genetic distance analysis of RAPD data were used to assess the extent of host specialization in 50 isolates of S. homoeocarpa from five turfgrass hosts. In UPGMA analysis and principal component analysis, the occurrence of host specialization was not readily apparent based on visual inspection. Genetic diversity analys...

To separate the unknown Streptomyces strains isolated from soil samples, the interspacer regions of 16S-23S rDNA of 14 isolates were amplified with PCR (polymerase chain reaction) and digested with three restriction endonucleases, namely, Bsp143I, HaeIII and MnlI. The restriction patterns were used for RFLP (restriction fragment length polymorphism) analysis. A dendrogram were constructed using...

In this work we consider hierarchical clustering algorithms, such as UPGMA, which follow the closest-pair joining scheme. We survey optimal O(n)-time implementations of such algorithms which use a ‘locally closest’ joining scheme, and specify conditions under which this relaxed joining scheme is equivalent to the original one (i.e. ‘globally closest’).

not ensure that their joint solutions do not interact. This is clearly an undesirable property that is not shared by methods that form groups based only on the spatial relationships of OTUs that are relatively close together. Classifications based on minimum spanning trees (e.g., by using the single-link clustering method) and the UPGMA clustering method are obvious examples of methods that do ...

MOTIVATION Clustering methods including k-means, SOM, UPGMA, DAA, CLICK, GENECLUSTER, CAST, DHC, PMETIS and KMETIS have been widely used in biological studies for gene expression, protein localization, sequence recognition and more. All these clustering methods have some benefits and drawbacks. We propose a novel graph-based clustering software called COMUSA for combining the benefits of a coll...

The Innovation of Artifacts is somewhat can be seen as a process of evolution. The paper presents an endeavor to view the evolution of artifact by using evolutionary concept of memetics. We showed the ways to build a phlyomemetic tree based on memes constituting an artifact to infer or estimate the evolutionary history and relationship between artifacts. UPGMA algorithm and the Shortest Tree Me...

Nine Random Amplified Polymorphic DNA (RAPD) primers showing polymorphic bands were used to determine the genetic relatedness among and within single individual plants of Lupinus pilosus and used for the construction of the dendrogram and the similarity matrix. A total of 1112 bands were obtained, 219 of which were polymorphic. Similarity values among the studied single individuals of Lupinus p...

SoRT(2) is a web server that allows the user to perform genome rearrangement analysis involving reversals, generalized transpositions and translocations (including fusions and fissions), and infer phylogenetic trees of genomes being considered based on their pairwise genome rearrangement distances. It takes as input two or more linear/circular multi-chromosomal gene (or synteny block) orders in...