Title
Integration of Clustering and Multidimensional Scaling to Determine Phylogenetic Trees as Spherical Phylograms Visualized in 3 Dimensions
Abstract
Phylogenetic analysis is commonly used to analyze genetic sequence data from fungal communities, while ordination and clustering techniques commonly are used to analyze sequence data from bacterial communities. However, few studies have attempted to link these two independent approaches. In this paper, we propose a method, which we call spherical phylogram (SP), to display the phylogenetic tree within the clustering and visualization result from a pipeline called DACIDR. In comparison with traditional tree display methods, the correlations between the tree and the clustering can be observed directly. In addition, we propose an algorithm called interpolative joining (IJ) to construct and visualize the SP in 3D space. In the experiments, we used the sum of branch lengths to quantify the general fit between the clustering and the phylogenetic tree in SP and Mantel tests to determine how well the same grouping of sequences was preserved between the clustering and the SP. Our results show that DACIDR has a classification accuracy that is similar to a phylogenetic tree generated using a multiple sequence alignment, while having much lower computational cost.
Year
DOI
Venue
2014
10.1109/CCGrid.2014.126
CCGrid
Keywords
DocType
ISSN
dacidr,pattern clustering,evolution (biological),phylogenetic tree,interpolation,sequence alignment,genetics,fungal communities,microorganisms,clustering techniques,pattern classification,sp,branch lengths,environmental genomics,microbial communities,genetic sequence data,multidimensional scaling,visualization,3d space,phylogenetic analysis,biology computing,sequence data analysis,data visualisation,ij,classification accuracy,bacterial communities,tree display methods,mantel tests,ordination,interpolative joining,spherical phylogram,clustering algorithms,phylogeny,mathematical model
Conference
2376-4414
Citations 
PageRank 
References 
3
0.41
11
Authors
7
Name
Order
Citations
PageRank
Yang Ruan11126.26
Geoffrey L. House230.41
Saliya Ekanayake3909.34
Ursel Schutte430.41
James D. Bever530.41
Haixu Tang668396.67
Geoffrey Fox74070575.38