<commit_before>[[https://github.com/BioInf-Wuerzburg/AliTV/blob/master/LICENSE][https://img.shields.io/github/license/mashape/apistatus.svg]]

** Build
[[https://travis-ci.org/BioInf-Wuerzburg/AliTV/][https://travis-ci.org/BioInf-Wuerzburg/AliTV.svg?branch=master]]
[[https://coveralls.io/github/BioInf-Wuerzburg/AliTV?branch=master][https://coveralls.io/repos/github/BioInf-Wuerzburg/AliTV/badge.svg?branch=master]]

** Homepage
[[http://bioinf-wuerzburg.github.io/AliTV][AliTV]]
** Installation

#+BEGIN_EXAMPLE
  git clone --recursive https://github.com/BioInf-Wuerzburg/AliTV
#+END_EXAMPLE
   
** Dependencies

- lastz or MUMmer
- Circos
- optional - blastn (for IR annotation)

** Usage
To get usage information
#+BEGIN_EXAMPLE
  AliTV --help
#+END_EXAMPLE

Example usage
#+BEGIN_EXAMPLE
  AliTV --query query.fa --reference reference.fa
#+END_EXAMPLE

** Output
By default, AliTV generates ten files in the output folder:

| <prefix>.txt             | The output of the whole genome alignment program in tabular format      |
| <prefix>.svg             | The circular map of the wga created by Circos in svg format             |
| <prefix>.png             | The circular map of the wga created by Circos in png format             |
| <prefix>.circos.conf     | The generated circos config file                                        |
| <prefix>.karyo           | The karyotype file for Circos                                           |
| <prefix>.link            | The link file for Circos                                                |
| <prefix>.high            | The highlight file for Circos                                           |
| <prefix>.wanted_ids      | The new IDs of sequences with illegal characters replaced by underscore |
| <prefix>_query.fasta     | A copy of the query fasta with adjusted IDs                             |
| <prefix>_reference.fasta | A copy of the reference fasta with adjusted IDs                         |

A demo of the new interactive HTML/JavaScript output can be found [[http://bioinf-wuerzburg.github.io/AliTV/d3/AliTV.html][here]].

** Input
Both the query and the reference file should be in fasta format.

** Citing AliTV

We have not yet submitted a manuscript.
Please use this repository to cite AliTV if you use it in your project.
[[https://zenodo.org/badge/latestdoi/12731/BioInf-Wuerzburg/AliTV][https://zenodo.org/badge/12731/BioInf-Wuerzburg/AliTV.svg]]

Please also consider citing:
 - lastz or MUMmer
 - Circos
 - BLAST (for IR annotation)

For a list of included libraries together with their respective licenses see the [[file:LICENSES/][LICENSES]] folder.
** Contact
If you have any questions or encounter problems or potential bugs, don't
hesitate to contact us. Either report [[https://github.com/BioInf-Wuerzburg/AliTV/issues][issues]] on github or write an email to:

- <NAME> - <EMAIL>






#+TITLE: AliTV manual
#+AUTHOR: <NAME>
#+EMAIL: <EMAIL>
#+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}
** Changelog
*** 0.3.7 <2016-06-02 Do><commit_msg>Add change log for 0.3.8<commit_after>[[https://github.com/BioInf-Wuerzburg/AliTV/blob/master/LICENSE][https://img.shields.io/github/license/mashape/apistatus.svg]]

** Build
[[https://travis-ci.org/BioInf-Wuerzburg/AliTV/][https://travis-ci.org/BioInf-Wuerzburg/AliTV.svg?branch=master]]
[[https://coveralls.io/github/BioInf-Wuerzburg/AliTV?branch=master][https://coveralls.io/repos/github/BioInf-Wuerzburg/AliTV/badge.svg?branch=master]]

** Homepage
[[http://bioinf-wuerzburg.github.io/AliTV][AliTV]]
** Installation

#+BEGIN_EXAMPLE
  git clone --recursive https://github.com/BioInf-Wuerzburg/AliTV
#+END_EXAMPLE
   
** Dependencies

- lastz or MUMmer
- Circos
- optional - blastn (for IR annotation)

** Usage
To get usage information
#+BEGIN_EXAMPLE
  AliTV --help
#+END_EXAMPLE

Example usage
#+BEGIN_EXAMPLE
  AliTV --query query.fa --reference reference.fa
#+END_EXAMPLE

** Output
By default, AliTV generates ten files in the output folder:

| <prefix>.txt             | The output of the whole genome alignment program in tabular format      |
| <prefix>.svg             | The circular map of the wga created by Circos in svg format             |
| <prefix>.png             | The circular map of the wga created by Circos in png format             |
| <prefix>.circos.conf     | The generated circos config file                                        |
| <prefix>.karyo           | The karyotype file for Circos                                           |
| <prefix>.link            | The link file for Circos                                                |
| <prefix>.high            | The highlight file for Circos                                           |
| <prefix>.wanted_ids      | The new IDs of sequences with illegal characters replaced by underscore |
| <prefix>_query.fasta     | A copy of the query fasta with adjusted IDs                             |
| <prefix>_reference.fasta | A copy of the reference fasta with adjusted IDs                         |

A demo of the new interactive HTML/JavaScript output can be found [[http://bioinf-wuerzburg.github.io/AliTV/d3/AliTV.html][here]].

** Input
Both the query and the reference file should be in fasta format.

** Citing AliTV

We have not yet submitted a manuscript.
Please use this repository to cite AliTV if you use it in your project.
[[https://zenodo.org/badge/latestdoi/12731/BioInf-Wuerzburg/AliTV][https://zenodo.org/badge/12731/BioInf-Wuerzburg/AliTV.svg]]

Please also consider citing:
 - lastz or MUMmer
 - Circos
 - BLAST (for IR annotation)

For a list of included libraries together with their respective licenses see the [[file:LICENSES/][LICENSES]] folder.
** Contact
If you have any questions or encounter problems or potential bugs, don't
hesitate to contact us. Either report [[https://github.com/BioInf-Wuerzburg/AliTV/issues][issues]] on github or write an email to:

- <NAME> - <EMAIL>






#+TITLE: AliTV manual
#+AUTHOR: <NAME>
#+EMAIL: <EMAIL>
#+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}
** Changelog
*** 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>
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