<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43614?offset=520 https://bioinformaticsonline.com/bookmarks/view/30698/itol-interactive-tree-of-life Tue, 31 Jan 2017 05:56:30 -0600 https://bioinformaticsonline.com/bookmarks/view/30698/itol-interactive-tree-of-life <![CDATA[iTOL: interactive Tree Of Life]]> Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized tree (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based.

image
There are several pre-computed trees available for display, including the main Tree Of Life, described in Ciccarelli, et al., 2006. In addition to the precomputed trees, users can upload and display personal trees and data, using the 'Data upload' page or through a personal user account.

Address of the bookmark: http://itol.embl.de/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35635/ete-3-reconstruction-analysis-and-visualization-of-phylogenomic-data Mon, 19 Feb 2018 06:46:15 -0600 https://bioinformaticsonline.com/bookmarks/view/35635/ete-3-reconstruction-analysis-and-visualization-of-phylogenomic-data <![CDATA[ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data]]> ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics.

The new features include

(i) building gene-based and supermatrix-based phylogenies using a single command,

(ii) testing and visualizing evolutionary models,

(iii) calculating distances between trees of different size or including duplications, and

(iv) providing seamless integration with the NCBI taxonomy database.

ETE is freely available at http://etetoolkit.org

Address of the bookmark: http://etetoolkit.org

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36368/d3-javascript-for-visualization Mon, 23 Apr 2018 08:42:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36368/d3-javascript-for-visualization <![CDATA[D3 javascript for visualization !]]> Welcome to the D3 gallery! More examples are available on bl.ocks.org/mbostock. If you want to share an example and don't have your own hosting, consider using Gist and bl.ocks.org. If you want to share or view live examples try vida.io.

Address of the bookmark: https://github.com/d3/d3/wiki/Gallery

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37982/raven-a-software-suite-for-matlab-that-allows-for-semi-automated-reconstruction-of-genome-scale-models Wed, 24 Oct 2018 22:38:05 -0500 https://bioinformaticsonline.com/bookmarks/view/37982/raven-a-software-suite-for-matlab-that-allows-for-semi-automated-reconstruction-of-genome-scale-models <![CDATA[RAVEN: a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models]]> The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Address of the bookmark: https://github.com/SysBioChalmers/RAVEN

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41209/juicebox-visualization-and-analysis-software-for-hi-c-data Fri, 21 Feb 2020 00:33:38 -0600 https://bioinformaticsonline.com/bookmarks/view/41209/juicebox-visualization-and-analysis-software-for-hi-c-data <![CDATA[Juicebox: Visualization and analysis software for Hi-C data]]> Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.

Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly.

GUI at https://aidenlab.org/juicebox/

Address of the bookmark: https://github.com/aidenlab/Juicebox

]]> Jit https://bioinformaticsonline.com/bookmarks/view/33693/circleator Sun, 25 Jun 2017 18:04:32 -0500 https://bioinformaticsonline.com/bookmarks/view/33693/circleator <![CDATA[Circleator]]> The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Sample Circleator image

Common uses of the tool include:

  • Displaying the sequence and/or genes in a GenBank flat file.
  • Highlighting differences and/or similarities in gene content between related organisms.
  • Comparing SNPs and indels between closely-related strains or serovars.
  • Comparing gene expression values across multiple samples or timepoints.
  • Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

  • Builds on BioPerl and the input file formats that it supports, including:
  • Accepts a number of other commonly-used datatypes and file formats:
    • BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
  • Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
  • Requires only a single configuration file whose layout mirrors that of the figure itself.
    • Predefined configuration files and "track" types are supplied for common datasets.
    • Advanced features allow limited analyses to be performed as a figure is drawn.
  • Includes an extensive set of regression tests.
  • Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35400/zpicture-a-dynamic-blastz-alignment-visualization Tue, 30 Jan 2018 16:03:08 -0600 https://bioinformaticsonline.com/bookmarks/view/35400/zpicture-a-dynamic-blastz-alignment-visualization <![CDATA[zPicture: A dynamic blastz alignment visualization]]> zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.

Address of the bookmark: https://zpicture.dcode.org/

]]> Archana Malhotra https://bioinformaticsonline.com/bookmarks/view/37259/epiviz-an-interactive-visualization-tool-for-functional-genomics-data Mon, 09 Jul 2018 05:27:39 -0500 https://bioinformaticsonline.com/bookmarks/view/37259/epiviz-an-interactive-visualization-tool-for-functional-genomics-data <![CDATA[Epiviz: an interactive visualization tool for functional genomics data.]]> Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library Wed, 09 Jan 2019 11:00:32 -0600 https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library <![CDATA[visNetwork: an R package for network visualization, using vis.js javascript library]]>

visNetwork is an R package for network visualization, using vis.js javascript library (http://visjs.org/). All remarks and bugs are welcome on github : https://github.com/datastorm-open/visNetwork.

Features

Based on htmlwidgets, so :

  • compatible with shiny, R Markdown documents, and RStudio viewer

The package proposes all the features available in vis.js API, and even more with special features for R :

  • easy to use
  • custom shapes, styles, colors, sizes, …
  • works smooth on any modern browser for up to a few thousand nodes and edges
  • interactivity controls (highlight, collapsed nodes, selection, zoom, physics, movement of nodes, tooltip, events, …)
  • visualize rpart tree

Address of the bookmark: https://datastorm-open.github.io/visNetwork/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44208/circos-visualization Mon, 06 Mar 2023 06:01:32 -0600 https://bioinformaticsonline.com/bookmarks/view/44208/circos-visualization <![CDATA[Circos visualization !]]> Circos visualization

https://wlcb.oit.uci.edu/modules/index.html

Address of the bookmark: https://wlcb.oit.uci.edu/NG-Circos

]]> BioStar