https://github.com/s-andrews/redotable

A dotplot application for DNA/RNA sequence
https://github.com/s-andrews/redotable

desktop-application genome-sequencing sequence-alignment sequence-to-sequence visualization

Last synced: 4 months ago
JSON representation

A dotplot application for DNA/RNA sequence

• Host: GitHub
• URL: https://github.com/s-andrews/redotable
• Owner: s-andrews
• License: gpl-3.0
• Created: 2018-08-01T08:00:37.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2022-11-28T16:10:56.000Z (over 1 year ago)
• Last Synced: 2024-01-17T03:18:23.250Z (6 months ago)
• Topics: desktop-application, genome-sequencing, sequence-alignment, sequence-to-sequence, visualization
• Language: Java
• Size: 388 KB
• Stars: 10
• Watchers: 3
• Forks: 1
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• repo-5916-awesome-genome-visualization - Redotable - genome-visualization/redotable.png) (Dotplot)
• awesome-genome-visualization - Redotable

README

        
![Redotable logo](https://raw.githubusercontent.com/s-andrews/redotable/master/uk/ac/babraham/redotable/resources/redotable_logo.png)

Re-dot-able is a dot-plotting application allowing for the visual comparisons of two sets of sequences.  It can work interactively, functioning as a desktop application, or can be run as a command line tool.

![Redotable screenshot](https://raw.githubusercontent.com/s-andrews/redotable/master/uk/ac/babraham/redotable/resources/redotable_screenshot.png)

We developed this initially to allow for the comparison of assembled bacterial sequences with reference genomes, but it can be applied to any comparison which involves large sequences.

Installation

============

You can download binary distributions of redotable from the project site at:

www.bioinformatics.babraham.ac.uk/projects/redotable/

Windows

-------

You will need to install the Oracle Java Runtime Environemnt from java.com

Once you have this installed you can download the redotable zip file from the [project web site](https://www.bioinformatics.babraham.ac.uk/projects/redotable/), and uncompress it somewhere on your machine.

To start the program just double click on re-dot-able.exe.

OSX

---

To allow redotable to run on OSX you will need to install the Oracle Java Development Kit which you should be able to get from [here](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)

Once that is installed you can download the redotable DMG file from the [project web page](https://www.bioinformatics.babraham.ac.uk/projects/redotable/).  If you double click on this it will open as a virtual disk and you will see the redotable application icon.  To install the program simply drag this icon out of the redotable virtual disk to a location on your computer (for example your Applications folder). You can then run the program by double clicking on the application.

Linux

-----

You will need a full java runtime environment installed on the machine you want to run redotable on.  Some distributions will install this by default, others install a cut-down version which can't run graphical applications.

To install a full JRE you can use:

**Ubuntu / Debian** `sudo apt install default-jre`

**CentOS / Redhat** `sudo yum install java-1.8.0-openjdk`

Once this is done you can download and uncompress the windows/linux zip file from the [project web page](https://www.bioinformatics.babraham.ac.uk/projects/redotable/).

You can then launch the program by using the `redotable` launch script in the root folder of the installation.

If you want to add this script to a folder in your path so you can launch the program from anywhere on your system then you will need to do this by creating a symlink to the launch script, **not** by copying it.

For example if you installed redotable into `/opt/redotable`, then to put the program into your path you would do:

`sudo ln -s /opt/redotable/redotable /usr/local/bin/`