alitv

Visualize whole genome alignments as linear maps

https://github.com/alitvteam/alitv

Repository

Visualize whole genome alignments as linear maps

README.org

** Tutorial
Read the documentation at [[http://alitv.readthedocs.io/en/latest/index.html][readthedocs]].

** Dependencies
 - A web browser
 - For the perl part, see [[https://github.com/AliTVTeam/AliTV-perl-interface][AliTV-perl-interface]]

** Installation
You do not need to install anything to try the interactive visualization of AliTV.
Just navigate to the [[https://alitvteam.github.io/AliTV/d3/AliTV.html][demo]] page to try all the features on an example dataset (seven chloroplast genomes).
You can also import your own json files on that page.
When loading your own data into AliTV it is not transferred to a server but remains on your local machine.

If you want to generate the json file for your genomes you can use the command line script alitv.pl as follows:
#+BEGIN_EXAMPLE
  # Install perl dependencies e.g. with cpan, cpanm or package manager (example: apt)
  # apt install libyaml-perl libhash-merge-perl bioperl
  git clone --recursive https://github.com/AliTVTeam/AliTV
#+END_EXAMPLE

** Usage
AliTV.pl can be called directly on your input files or in advanced mode supplying a yaml configuration file.
The output is a json object as required by the visualization part of AliTV (see [[https://alitvteam.github.io/AliTV/d3/doc/AliTV.html][details]]) in the file .json (project can be set via command line parameter, otherwise a random name is generated). For more details about ~alitv.pl~ please see [[https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/doc/alitv.md][the documentation]].

Simple mode: Just supply your files and redirect to json file
#+BEGIN_EXAMPLE
  cd AliTV-perl-interface
  perl bin/alitv.pl --project simple data/chloroset/*.fasta
#+END_EXAMPLE

Advanced mode: Supply a config yaml file
#+BEGIN_EXAMPLE
  cd AliTV-perl-interface
  perl bin/alitv.pl --project advanced data/chloroset/input.yml
#+END_EXAMPLE

** Input
Input for the simple mode should be in one of the [[http://bioperl.org/howtos/SeqIO_HOWTO.html#item5][Bioperl supported formats]] (currently 42 different).
Annotation files can be supplied in tsv format (have to be specified in the yml file, [[https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/data/chloroset/ndh.tsv][example file for ndh genes]]).
Documentation for the yaml file is soon to be added for now consult this [[https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/data/chloroset/input.yml][example file]] for usage information.

** Output
By default, AliTV generates a configuration file (yaml format) if none is supplied, a log file and a json string on standard out.
The json can then be visualized with AliTV on the [[https://alitvteam.github.io/AliTV/d3/AliTV.html][demo]] page or locally in [[d3/AliTV.html]].
The format of the json file is specified in the [source documentation](https://alitvteam.github.io/AliTV/d3/doc/AliTV.html) relevant members are "conf", "data", and "filters".

** Homepage
For further information visit the [[http://alitvteam.github.io/AliTV][homepage]].

** Citing AliTV

An article about AliTV has been published in [[https://peerj.com/articles/cs-116/][PeerJ Computer Science]] [[https://peerj.com/articles/cs-116/][https://img.shields.io/badge/DOI-10.7717%2Fpeerj--cs.116-blue.svg]]
Please cite this article if you use AliTV in your project.
Additionally the software in any specific version can be cited via its zenodo doi, latest:
[[https://zenodo.org/badge/latestdoi/12731/AliTVTeam/AliTV][https://zenodo.org/badge/12731/AliTVTeam/AliTV.svg]]

Please also cite:
 - lastz
 - bioperl

** Contact
If you have any questions or encounter problems or potential bugs, don't
hesitate to contact us. Either report [[https://github.com/AliTVTeam/AliTV/issues][issues]] on github or write an email to:

- Markus Ankenbrand - markus.ankenbrand@uni-wuerzburg.de

** License
[[https://github.com/AliTVTeam/AliTV/blob/master/LICENSE][https://img.shields.io/github/license/mashape/apistatus.svg]]

AliTV itself is available under MIT license.
The licenses of included libraries might differ, please see [[LICENSES/README.org]] for details.
** Build
[[https://travis-ci.org/AliTVTeam/AliTV/][https://travis-ci.org/AliTVTeam/AliTV.svg?branch=master]]
[[https://coveralls.io/github/AliTVTeam/AliTV?branch=master][https://coveralls.io/repos/github/AliTVTeam/AliTV/badge.svg?branch=master]]

** Repo Status
[[https://www.repostatus.org/#inactive][https://www.repostatus.org/badges/latest/inactive.svg]]
Inactive  The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.

** Changelog
*** Next release
 - Fix karyo shift error with big number of genomes
 - Fix link length filter (#146)
 - Add CITATION.cff
 - Add repo status badge
*** 1.0.6 <2018-06-08>
 - Update AliTV-perl-interface to v1.0.6
*** 1.0.5 <2018-05-15>
 - Add experimental auto-ordering
 - Fix context menu bug
*** 1.0.4 <2018-01-05>
 - Use karyo names rather than ids in web interface
 - Add google analytics to collect usage stats (with opt-out possibility)
*** 1.0.3 <2017-06-16>
 - Fix split feature bug (#131)
 - Add citation info
*** 1.0.2 <2017-04-25>
 - Add documentation of perl part (rtd)
 - Add demo sets bacteria, chromosomes
 - Fix svg namespace (#116)
 - Remove genome color gradient from chloro demo
 - Include perl part version 1.0.2
*** 1.0.1 <2017-04-20 Do>
 - Include perl part version 1.0.1
*** 1.0.0 <2017-04-13 Do>
 - Include perl part version 1.0.0
*** 0.4.1 <2016-08-05 Fr>
 - Fix corner cases for move chromosome left/right
 - Fix corner cases for move genome up/down
 - Add linkOpacity setting (#104)
 - Remove circular from headline (#102)
 - Fix special characters in id bug (#108)
 - Add feature labels
 - Update perl part to version 0.1.7
*** 0.4.0 <2016-06-18 Sa>
 - Include new perl interface
 - Update documentation
*** 0.3.9 <2016-06-09 Do>
 - Move to AliTVTeam organization
*** 0.3.8 <2016-06-06 Mo>
 - Update bootstrap-select to version 1.10.0
 - Update colorpicker to version 2.3.2
 - Update bootstrap to version 3.3.6
 - Update jQuery-UI to version 1.11.4
 - Update jQuery to version 2.2.4
 - Update d3.js to version 3.5.17
*** 0.3.7 <2016-06-02 Do>
 - Improve general layout and style
 - Improve tab structure of Advanced Settings (#89)
 - Fix getter/setter for shifting chromosomes (#91)
 - Display name and genome of a seq (#96)
*** 0.3.6 <2015-11-02 Mo>
 - Highlight active slider range (#84)
 - Update slider range (#85)
 - Fix feature hiding bug (#87)
 - Fix tree drawing bug (#88)
*** 0.3.5 <2015-09-24 Do>
 - Add version number to html page
 - Auto adjust tree representation when reordering genomes
 - Warn if tree is not concordant with genome order
 - Legend for biological feature types
 - Color scale for link identity
*** 0.3.4 <2015-09-16 Mi>
 - Add custom features via the interface
*** 0.3.3 <2015-09-11 Fr>
 - Bug fix in template
*** 0.3.2 <2015-09-11 Fr>
 - rotation of circular sequences
 - dynamic (biological) feature menus
 - code cleanup
*** 0.3.1 <2015-08-13 Do>
 - Strand specific features
 - Reset for genome zooming
 - Libraries for contextMenu are update with generateJSONFiles.pl
 - Fix #52: allow hiding of features with non-unique names
 - Add new alerts and error messages
*** 0.3 <2015-07-31 Fr>
 - Show selected genome regions (independent)
 - Horizontal scroll bar
 - Add complete tab structure for the interface
 - Add context menus for chromosomes, features and links
 - Allow reordering of genomes and chromosomes by using the context menus
 - Allow specific hiding of features, links and chromosomes
*** 0.2.1 <2015-07-16 Do>
 - Added MIT License
 - Included License information for third party libraries
*** 0.2.0 <2015-07-16 Do>
 - allow for input as tsv and bed files as alternative to fasta files
 - demo data added - seven chloroplast genomes
 - documentation added
 - test cases added
 - added interactive JavaScript output
 - renamed to Alignment Toolbox and Visualization (AliTV)
*** 0.1.0 <2015-01-31 Sa>
 - First release of the wgaPipeline code.
 - Automated whole genome alignment and circos visualization from two fasta files.

#+TITLE: AliTV
#+AUTHOR: Markus Ankenbrand
#+EMAIL: markus.ankenbrand@uni-wuerzburg.de
#+LANGUAGE: en
#+OPTIONS: ^:nil date:nil H:2
#+LaTeX_CLASS: scrartcl
#+LaTeX_CLASS_OPTIONS: [a4paper,12pt,headings=small]
#+LaTeX_HEADER: \setlength{\parindent}{0pt}
#+LaTeX_HEADER: \setlength{\parskip}{1.5ex}
#+LATEX_HEADER: \renewcommand{\familydefault}{\sfdefault}

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite both the software and the paper (see preferred-citation).
authors:
  - family-names: Ankenbrand
    given-names: "Markus J"
    orcid: 0000-0002-6620-807X
    affiliation: "Center for Computational and Theoretical Biology, University of Würzburg, Germany"
    email: markus.ankenbrand@uni-wuerzburg.de
  - family-names: Hohlfeld
    given-names: "Sonja CY"
    affiliation: "Center for Computational and Theoretical Biology, University of Würzburg, Germany"
  - family-names: Hackl
    given-names: Thomas
    orcid: 0000-0002-0022-320X
    affiliation: "Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA"
  - family-names: Förster
    given-names: Frank
    orcid: 0000-0003-4166-5423
    affiliation: "Fraunhofer Institute for Molecular Biology and Applied Ecology IME: Gießen"
    email: frank.foerster@ime.fraunhofer.de
title: AliTV
version: 1.0.6
doi: 10.5281/zenodo.1285849
date-released: 2018-06-08
repository-code: https://github.com/AliTVTeam/AliTV
keywords:
  - Comparative genomics
  - Alignment
  - Visualization 
license: MIT
url: https://alitvteam.github.io/AliTV
preferred-citation:
  type: article
  scope: Cite this paper if you used AliTV in your research
  authors:
    - family-names: Ankenbrand
      given-names: Markus J
    - family-names: Hohlfeld
      given-names: Sonja CY
    - family-names: Hackl
      given-names: Thomas
    - family-names: Förster
      given-names: Frank
  title: "AliTV - interactive visualization of whole genome comparisons"
  year: 2017
  journal: PeerJ Computer Science
  volume: 3
  issue: e116
  doi: 10.7717/peerj-cs.116
  url: https://doi.org/10.7717/peerj-cs.116

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