Tree (data structure)

About: Tree (data structure) is a research topic. Over the lifetime, 44931 publications have been published within this topic receiving 749669 citations. The topic is also known as: tree structure & tree.

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.

Abstract: MOTIVATION Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. RESULTS We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. AVAILABILITY AND IMPLEMENTATION The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng. RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Defining clusters from a hierarchical cluster tree

Abstract: Summary: Hierarchical clustering is a widely used method for detecting clusters in genomic data. Clusters are defined by cutting branches off the dendrogram. A common but inflexible method uses a constant height cutoff value; this method exhibits suboptimal performance on complicated dendrograms. We present the Dynamic Tree Cut R package that implements novel dynamic branch cutting methods for detecting clusters in a dendrogram depending on their shape. Compared to the constant height cutoff method, our techniques offer the following advantages: (1) they are capable of identifying nested clusters; (2) they are flexible—cluster shape parameters can be tuned to suit the application at hand; (3) they are suitable for automation; and (4) they can optionally combine the advantages of hierarchical clustering and partitioning around medoids, giving better detection of outliers. We illustrate the use of these methods by applying them to protein–protein interaction network data and to a simulated gene expression data set. Availability: The Dynamic Tree Cut method is implemented in an R package available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting Contact: stevitihit@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online.

Tree visualization with tree-maps: 2-d space-filling approach

Abstract: The traditional approach to representing tree structures is as a rooted, directed graph with the root node at the top of the page and children nodes below the parent node with lines connecting them (Figure 1). Knuth (1968, p. 305-313) has a long discussion about this standard representation, especially why the root is at the top and he offers several alternatives including brief mention of a space-filling approach. However, the remainder of his presentation and most other discussions of trees focus on various node and edge representations. By contrast, this paper deals with a two-dimensional (2-d) space-filling approach in which each node is a rectangle whose area is proportional to some attribute such as node size.