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A reference guide for tree analysis and visualization
2010
BioData Mining
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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
2018
GigaScience
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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]
2022
bioRxiv
pre-print
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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
2011
BMC Bioinformatics
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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
2010
Algorithms for Molecular Biology
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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
2014
Nucleic Acids Research
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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
2015
Proceedings of the 2015 ACM Symposium on Document Engineering - DocEng '15
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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
2008
BMC Bioinformatics
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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
1989
Contemporary Psychology
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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
2001
Proceedings of the 39th Annual Meeting on Association for Computational Linguistics - ACL '01
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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
2009
IEEE Transactions on Visualization and Computer Graphics
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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
2015
Computer graphics forum (Print)
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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
2004
BMC Bioinformatics
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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
2012
Visualization and Data Analysis 2012
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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]
2020
Embodying Data
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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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