More at http://www.broadinstitute.org/annotation/medea/

Address of the bookmark: http://www.broadinstitute.org/annotation/medea/

Blobsplorer is unlikely to be of use on its own as it requires contig data to be supplied in a format that involves considerable preprocessing (see below for a description). The easiest way to use Blobsplorer is as part of a workflow using scripts from here.

Address of the bookmark: http://nematodes.org/martin/blobsplorer/blobsplorer.html

Keep scrolling. Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.

Address of the bookmark: http://www.r2d3.us/visual-intro-to-machine-learning-part-1/

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/

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

Address of the bookmark: http://www.cmbb.arizona.edu/?page_id=250

For further details about the original technique see the UpSet website. You can also check out the UpSetR shiny app. Here is the source code for the shiny wrapper.

A Python package called py-upset to create UpSet plots has been created by GitHub user ImSoErgodic.

Address of the bookmark: https://github.com/hms-dbmi/UpSetR/

SynVisio requires two files to run:

• The simplified gff file that was used as an input for a McScanX query.
• The collinearity file generated as an output by McScanX for the same input query.
• Optional track file in bedgraph format to annotate the generated charts.

SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.

Address of the bookmark: https://synvisio.github.io/#/

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:
  • GenBank flat files, GFF, FASTA
• 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