{"id":33051421,"url":"https://github.com/s-andrews/redotable","last_synced_at":"2026-01-18T07:45:47.523Z","repository":{"id":63891949,"uuid":"143123624","full_name":"s-andrews/redotable","owner":"s-andrews","description":"A dotplot application for DNA/RNA sequence","archived":false,"fork":false,"pushed_at":"2022-11-28T16:10:56.000Z","size":397,"stargazers_count":10,"open_issues_count":5,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-06T21:26:23.111Z","etag":null,"topics":["desktop-application","genome-sequencing","sequence-alignment","sequence-to-sequence","visualization"],"latest_commit_sha":null,"homepage":null,"language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/s-andrews.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-08-01T08:00:37.000Z","updated_at":"2024-01-12T18:06:59.000Z","dependencies_parsed_at":"2023-01-14T12:15:18.703Z","dependency_job_id":null,"html_url":"https://github.com/s-andrews/redotable","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/s-andrews/redotable","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/s-andrews%2Fredotable","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/s-andrews%2Fredotable/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/s-andrews%2Fredotable/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/s-andrews%2Fredotable/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/s-andrews","download_url":"https://codeload.github.com/s-andrews/redotable/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/s-andrews%2Fredotable/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28533172,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T00:39:45.795Z","status":"online","status_checked_at":"2026-01-18T02:00:07.578Z","response_time":98,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["desktop-application","genome-sequencing","sequence-alignment","sequence-to-sequence","visualization"],"created_at":"2025-11-14T03:00:27.113Z","updated_at":"2026-01-18T07:45:47.512Z","avatar_url":"https://github.com/s-andrews.png","language":"Java","funding_links":[],"categories":["Dotplot"],"sub_categories":[],"readme":"![Redotable logo](https://raw.githubusercontent.com/s-andrews/redotable/master/uk/ac/babraham/redotable/resources/redotable_logo.png)\n\nRe-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.\n\n![Redotable screenshot](https://raw.githubusercontent.com/s-andrews/redotable/master/uk/ac/babraham/redotable/resources/redotable_screenshot.png)\n\nWe 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.\n\nInstallation\n============\n\nYou can download binary distributions of redotable from the project site at:\n\nwww.bioinformatics.babraham.ac.uk/projects/redotable/\n\nWindows\n-------\nYou will need to install the Oracle Java Runtime Environemnt from java.com\n\nOnce 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.\n\nTo start the program just double click on re-dot-able.exe.\n\nOSX\n---\nTo 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)\n\nOnce 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.\n\nLinux\n-----\nYou 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.\n\nTo install a full JRE you can use:\n\n**Ubuntu / Debian** `sudo apt install default-jre`\n\n**CentOS / Redhat** `sudo yum install java-1.8.0-openjdk`\n\nOnce 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/).\n\nYou can then launch the program by using the `redotable` launch script in the root folder of the installation.\n\nIf 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.\n\nFor example if you installed redotable into `/opt/redotable`, then to put the program into your path you would do:\n\n`sudo ln -s /opt/redotable/redotable /usr/local/bin/`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fs-andrews%2Fredotable","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fs-andrews%2Fredotable","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fs-andrews%2Fredotable/lists"}