<commit_before>| ****

| **Version 0.3.1**

|image|

About AliTV
===========

AliTV (Alignment Toolbox & Visualization) is a free software for
visualizing whole genome alignments as circular or linear maps. The
figure is presented on a HTML-page with an easy-to-use graphical user
interface. Comparisons between multiple genomic regions can be
generated, interactively analyzed and exported as svg.

Installation
============

Tutorial I: Simple comparasion of chloroplast genomes
=====================================================

In this example chloroplast genomes of seven parasitic and non-parasitic
plants are compared and analyzed with AliTV. The files needed for this
tutorial are used as the default data, this means you must not import
them.

Otherwise the files are available to download from...

Visualizing the Whole-Genome Alignment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  Open ``AliTV.html`` with your favourite webbrowser. When you use
   AliTV the first time the chloroplast data are used as the default
   data.

   .. figure:: showLabels.png
      :alt: The AliTV image using the default configuration.

      The AliTV image using the default configuration.
-  As you can see seven chloroplast genomes and the alignments between
   adjacent genomes are visualized. The genome of *N. tabacum* is
   splitted in two parts.

-  The phylogenetic tree represents the relationship between the
   analyzed genomes.

Create figure
^^^^^^^^^^^^^

-  For using the figure you have to download it. Click for saving the
   picture.

-  Open the folder where you saved the AliTV image and open it with your
   favourite image-viewer.<commit_msg>Fix typo<commit_after>| ****

| **Version 0.3.1**

|image|

About AliTV
===========

AliTV (Alignment Toolbox & Visualization) is a free software for
visualizing whole genome alignments as circular or linear maps. The
figure is presented on a HTML-page with an easy-to-use graphical user
interface. Comparisons between multiple genomic regions can be
generated, interactively analyzed and exported as svg.

Installation
============

Tutorial I: Simple comparasion of chloroplast genomes
=====================================================

In this example chloroplast genomes of seven parasitic and non-parasitic
plants are compared and analyzed with AliTV. The files needed for this
tutorial are used as the default data, this means you need not import
them.

Otherwise the files are available to download from...

Visualizing the Whole-Genome Alignment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-  Open ``AliTV.html`` with your favourite webbrowser. When you use
   AliTV the first time the chloroplast data are used as the default
   data.

   .. figure:: showLabels.png
      :alt: The AliTV image using the default configuration.

      The AliTV image using the default configuration.
-  As you can see seven chloroplast genomes and the alignments between
   adjacent genomes are visualized. The genome of *N. tabacum* is
   splitted in two parts.

-  The phylogenetic tree represents the relationship between the
   analyzed genomes.

Create figure
^^^^^^^^^^^^^

-  For using the figure you have to download it. Click for saving the
   picture.

-  Open the folder where you saved the AliTV image and open it with your
   favourite image-viewer.
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