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A reference guide for tree analysis and visualization

Georgios A Pavlopoulos, Theodoros G Soldatos, Adriano Barbosa-Silva, Reinhard Schneider
2010 BioData Mining  
In this study, we review tools that are currently available for the visualization of biological trees and analysis, mainly developed during the last decade.  ...  For example, the current phylogenetic tree visualization tools are not able to display easy to understand large scale trees with more than a few thousand nodes.  ...  The next section gives an overview of the most widely used tree-viewers for the analysis and visualization of data, primarily developed for phylogenetic analysis purposes, and covers mostly recent visualization  ... 
doi:10.1186/1756-0381-3-1 pmid:20175922 pmcid:PMC2844399 fatcat:k2k6u72nandljivhdbxvstuy2u

Aequatus: an open-source homology browser

Anil S Thanki, Nicola Soranzo, Javier Herrero, Wilfried Haerty, Robert P Davey
2018 GigaScience  
We also offer Aequatus.js, a reusable JavaScript module that fulfills the visualization aspects of Aequatus, available within the Galaxy web platform as a visualization plug-in, which can be used to visualize  ...  gene trees generated by the GeneSeqToFamily workflow.  ...  In this gene tree view, users are able to select a gene from a given species as a "guide gene," and the homologous genes discovered through the comparative analysis are shown with respect to this guide  ... 
doi:10.1093/gigascience/giy128 pmid:30395211 pmcid:PMC6251984 fatcat:ft4xlirnufhbnady4qwrzlk2um

PanGraph: scalable bacterial pan-genome graph construction [article]

Nicholas Noll, Marco Molari, Richard Neher
2022 bioRxiv   pre-print
The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into a several common formats for either downstream analysis or immediate  ...  visualization.  ...  ACKNOWLEDGEMENT We are grateful to Boris Shraiman for stimulating discussions. This study was funded by the University of Basel and the NSF.  ... 
doi:10.1101/2022.02.24.481757 fatcat:jubzs7h4qjelvh6h4qdgu7aj2e

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation

Catherine L Anderson, Cory L Strope, Etsuko N Moriyama
2011 BMC Bioinformatics  
Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications.  ...  Evaluating the quality of MSA reconstruction is often hindered by the lack of good reference MSAs. The use of sequence evolution simulation can provide such reference MSAs.  ...  This further assists comparative analysis of MSAs based on the "true" reference alignment where insertion and deletion events can be mapped individually onto both the guide tree and the true MSA.  ... 
doi:10.1186/1471-2105-12-184 pmid:21600033 pmcid:PMC3133551 fatcat:yp2metp2cjf6bmf7hmdpe3mqba

On the use of cartographic projections in visualizing phylo-genetic tree space

Kenneth Sundberg, Mark Clement, Quinn Snell
2010 Algorithms for Molecular Biology  
We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure.  ...  Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis.  ...  If it is not the visualization will not be able to be used in real time to guide a search. • The visualization should reveal exploitable structure.  ... 
doi:10.1186/1748-7188-5-26 pmid:20529355 pmcid:PMC2891783 fatcat:dybcurclqnd4rn7oklflwr62v4

POSA: a user-driven, interactive multiple protein structure alignment server

Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe, Adam Godzik
2014 Nucleic Acids Research  
This interface allows users to take advantage of their intuition and biological insights to improve the alignment and guide it toward a biologically relevant solution.  ...  The second improvement is an interactive visualization with options that allow the user to view all superposed structures in one window (a typical solution for visualizing results of multiple structure  ...  ACKNOWLEDGMENT We thank Drs Alexey Eroshkin and Lukasz Jaroszewski of Sanford-Burnham Medical Research Institute, La Jolla, CA, for their suggestions for the POSA upgrade.  ... 
doi:10.1093/nar/gku394 pmid:24838569 pmcid:PMC4086100 fatcat:quojw6yewncvzksa5t6rkyre6m

MSoS

Mira Sarkis, Cyril Concolato, Jean-Claude Dufourd
2015 Proceedings of the 2015 ACM Symposium on Document Engineering - DocEng '15  
In this paper we describe a multiscreen-oriented approach for segmenting web pages. The segmentation is an automatic and hybrid visual and structural method.  ...  Results are compared with one seg-mentation method from the literature and with a ground truth manually created.  ...  For instance the hybrid VIPS [1] , based on the joint DOM and visual analysis, utilizes both structural information in the DOM tree and visual cues to semantically segment a page.  ... 
doi:10.1145/2682571.2797090 dblp:conf/doceng/SarkisCD15 fatcat:fqgud6abijckjmllg7tlhf3glm

Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles

Yin-Jing Tien, Yun-Shien Lee, Han-Ming Wu, Chun-Houh Chen
2008 BMC Bioinformatics  
The hierarchical clustering tree (HCT) with a dendrogram [1] and the singular value decomposition (SVD) with a dimension-reduced representative map [2] are popular methods for two-way sorting the gene-by-array  ...  The resulting algorithm automatically integrates the desirable properties of each method so that users have access to a clustering and visualization environment for gene expression profiles that preserves  ...  Acknowledgements The authors are grateful to Donald Ylvisaker, Konan Peck, Chiun-How Kao, and ShengLi Tzeng for valuable suggestions and assistance.  ... 
doi:10.1186/1471-2105-9-155 pmid:18366693 pmcid:PMC2322988 fatcat:w7sh7sh6cvcajh44naopzmbsji

Review of Strategic Planning for Public and Nonprofit Organizations: A Guide to Strengthening and Sustaining Organizational Achievement

No authorship indicated
1989 Contemporary Psychology  
This adaptation of the House-Tree—Person technique requires children to draw a house, a tree, and an active person, all on the same page.  ...  References. Index. D. J. Hand and C. C. Taylor. Multivariate Analysis of Variance and Repeated Mea- sures: A Practical Approach for Behav- ioural Scientists. London: Chapman & Hall, 1987. 262 pp.  ... 
doi:10.1037/027983 fatcat:bvovqttakjfxxnjmwjciyfgn5m

A machine learning approach to the automatic evaluation of machine translation

Simon Corston-Oliver, Michael Gamon, Chris Brockett
2001 Proceedings of the 39th Annual Meeting on Association for Computational Linguistics - ACL '01  
This approach can be used to evaluate an MT system, tracking improvements over time; to aid in the kind of failure analysis that can help guide system development; and to select among alternative output  ...  We present a machine learning approach to evaluating the wellformedness of output of a machine translation system, using classifiers that learn to distinguish human reference translations from machine  ...  Acknowledgements Our thanks go to Eric Ringger and Max Chickering for programming assistance with the tools used in building and evaluating the decision trees, and to Mike Carlson for help in sampling  ... 
doi:10.3115/1073012.1073032 dblp:conf/acl/Corston-OliverGB01 fatcat:bqzsnnwmhzef5on7ojix27fejm

Visualizing the Intellectual Structure with Paper-Reference Matrices

Jian Zhang, Chaomei Chen, Jiexun Li
2009 IEEE Transactions on Visualization and Computer Graphics  
Visualizing the intellectual structure of scientific domains using co-cited units such as references or authors has become a routine for domain analysis.  ...  Instead of using a reference-reference matrix, we directly use the original paper-reference matrix as the information source, and transform the paper-reference matrix into an FP-tree and visualize it in  ...  Thomson Reuters provides the bibliographic data for the analysis. We also thank Michael S. Vogeley, Danny Pan and John Parejko for their constructive suggestions on the SDSS case study.  ... 
doi:10.1109/tvcg.2009.202 pmid:19834184 fatcat:noirwbzehrfuvjpm5pddejtjyy

State-of-the-Art in GPU-Based Large-Scale Volume Visualization

Johanna Beyer, Markus Hadwiger, Hanspeter Pfister
2015 Computer graphics forum (Print)  
Modern techniques in this field have brought about a sea change in how interactive visualization and analysis of giga-, tera-, and petabytes of volume data can be enabled on GPUs.  ...  In addition to combining the parallel processing power of GPUs with out-of-core methods and data streaming, a major enabler for interactivity is making both the computational and the visualization effort  ...  For a more in-depth discussion of the visualization and visual analysis of multi-faceted scientific data we refer the reader to a recent comprehensive survey [KH13] .  ... 
doi:10.1111/cgf.12605 fatcat:3dlv7zvzm5dx7nxqgfglp5vew4

GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy
2004 BMC Bioinformatics  
We have created a web-based tool for data analysis and data visualization for sets of genes called GOTree Machine (GOTM).  ...  GOTree Machine generates a GOTree, a tree-like structure to navigate the Gene Ontology Directed Acyclic Graph for input gene sets.  ...  Crawford for critical evaluation of this manuscript and Suzanne H. Baktash for helpful comments.  ... 
doi:10.1186/1471-2105-5-16 pmid:14975175 pmcid:PMC373441 fatcat:a6e3qs6mf5hhrei7ccrpw476su

Comparison of open-source visual analytics toolkits

John R. Harger, Patricia J. Crossno, Pak Chung Wong, David L. Kao, Ming C. Hao, Chaomei Chen, Robert Kosara, Mark A. Livingston, Jinah Park, Ian Roberts
2012 Visualization and Data Analysis 2012  
So we expanded our study to include information visualization, graph analysis, and statistical packages.  ...  We examine three aspects of each toolkit: visualization functions, analysis capabilities, and development environments.  ...  format. 29 The documentation field lists the available documentation, such as tutorials, user's guides, reference manuals and online API documentation.  ... 
doi:10.1117/12.911901 dblp:conf/vda/HargerC12 fatcat:5u7oj7764ngfnowzbmsscfjftm

Overview of Data Visualization [chapter]

Qi Li
2020 Embodying Data  
Humans often use trees as a symbol to represent classification of the natural world (Lima, 2011) . In visualization, tree can also refer to "Tree-Map" visualization (Johnson & Shneiderman, 1999) .  ...  For example, The Diagram Displays a Relationship and Information Flow for a Business System Analysis by Gerald Lohse emphasizes that the addition of background shading could enhance the understandability  ... 
doi:10.1007/978-981-15-5069-0_2 fatcat:d7uhatondbgnle2qa7ualduqje
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