Tree (set theory)
View article: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era Open
IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded …
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Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation Open
The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tre…
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UFBoot2: Improving the Ultrafast Bootstrap Approximation Open
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving…
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Interactive Tree Of Life (iTOL) v4: recent updates and new developments Open
The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new datase…
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Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees Open
Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten…
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W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis Open
This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, bina…
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<span>ggtree</span> : an <span>r</span> package for visualization and annotation of phylogenetic trees with their covariates and other associated data Open
Summary We present an r package, ggtree , which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick , nexus , NHX , phylip and jplace forma…
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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference Open
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…
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Tractatus Logico-Philosophicus Open
Tractatus Logico-Philosophicus by Ludwig Wittgenstein: Three parallel tree-structured editions. (1) Tree-structured arrangement of the German text, edited by David G. Stern, Joachim Schulte and Katia Saporiti. (2) Tree-structured arrangeme…
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ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules Open
The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macrom…
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PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools Open
PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms across the tree of life. We report the improvements we have made t…
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Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool Open
The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 6 introduces a modern…
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MUMmer4: A fast and versatile genome alignment system Open
The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major release of MUMmer version 3 in 2004, it has been applied to many types of probl…
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ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data Open
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous imp…
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Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices Open
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under i…
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<span>TNT</span> version 1.5, including a full implementation of phylogenetic morphometrics Open
Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes…
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Classification Based on Decision Tree Algorithm for Machine Learning Open
Decision tree classifiers are regarded to be a standout of the most well-known methods to data classification representation of classifiers. Different researchers from various fields and backgrounds have considered the problem of extending…
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PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API Open
PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-coding genes from all domains of life. The evolutionary classification is b…
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Efficient kNN Classification With Different Numbers of Nearest Neighbors Open
nearest neighbor (kNN) method is a popular classification method in data mining and statistics because of its simple implementation and significant classification performance. However, it is impractical for traditional kNN methods to assig…
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The R+-Tree: A Dynamic Index for Multi-Dimensional Objects Open
The problem of indexing multidimensional objects is considered. First, a classification of existing methods is given along with a discussion of the major issues involved in multidimensional data indexing. Second, a variation to Guttman’s R…
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End-to-End Relation Extraction using LSTMs on Sequences and Tree Structures Open
We present a novel end-to-end neural model to extract entities and relations between them.Our recurrent neural network based model captures both word sequence and dependency tree substructure information by stacking bidirectional treestruc…
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Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation Open
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their util…
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African Journal of Environmental Science and Technology Open
Air quality assessment of carbon monoxide, nitrogen dioxide and sulfur dioxide levels in Blantyre, Malawi: a statistical approach to a stationary environmental monitoring station
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Clustering trees: a visualization for evaluating clusterings at multiple resolutions Open
Clustering techniques are widely used in the analysis of large datasets to group together samples with similar properties. For example, clustering is often used in the field of single-cell RNA-sequencing in order to identify different cell…
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V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants Open
We present V.PhyloMaker, a freely available package for R designed to generate phylogenies for vascular plants. The mega‐tree implemented in V.PhyloMaker (i.e. GBOTB.extended.tre), which was derived from two recently published mega‐trees a…
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Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees Open
Evolview is an interactive tree visualization tool designed to help researchers in visualizing phylogenetic trees and in annotating these with additional information. It offers the user with a platform to upload trees in most common tree f…
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GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens Open
Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static “GrapeTree Layout” algorithm that su…
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HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing Open
Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth of the underlying phylogenetic tree summa…
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Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees Open
tvBOT is a user-friendly and efficient web application for visualizing, modifying, and annotating phylogenetic trees. It is highly efficient in data preparation without requiring redundant style and syntax data. Tree annotations are powere…
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Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies Open
Species tree reconstruction is complicated by effects of incomplete lineage sorting, commonly modeled by the multi-species coalescent model (MSC). While there has been substantial progress in developing methods that estimate a species tree…