logoAliTV  Visualize multiple whole genome alignments as linear maps

AliTV (Alignment Toolbox and Visualization) is a software for visualizing Whole Genome Alignments. It generates publication-ready figures which can be used for the easy comparision of complete genomes. AliTV stands out due to its interactive functions for analyzing the alignments directly onto the figure.

Please cite this article when using AliTV. The source code in any specific version can additionally be cited using the zenodo doi (latest: ).

If you need help with AliTV, please checkout the documentation, website or the repository on GitHub.

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Auto-order (beta)
Order chromosomes/contigs automatically by using the following heuristic:
  1. Assume genome with longest chromosome is the reference
  2. Reverse order of reference (if it was ordered by size, the largest chromosome comes first now)
  3. Order each chromosome of non-reference genome by the position of the largest hit to the reference
  4. Reverse each chromosome where the largest hit to the reference is twisted
Warning: The current order function is experimental and implemented in ES6 so if you are using an old browser it might not work.
Use JSONEditor
By using JSONEditor you can change all parameters directly in the structure of the conf-, data- or filters-object.
Shift chromosomes:
Demo data:
Filter links by their identity:

Filter links by their length:

Invisible links:
Invisible features:
Invisible chromosomes:
Define the feature group:
Choose form:
Rect
Arrow
Set color:
Choose orientation:
Left
Right
Width of tree (px):
Choose Your layout:
linear Linear Layout
circular Circular Layout
Set the SVG height and width:
Height:
Width:
Change parameters for chromosomes:
Spacer between chromosomes (bp):
Height of chromosomes (px):
Distance between ticks (bp):
Define a custome color range between color1 and color2 for the genomes:
Color 1
Color 2
Change parameters for links:
Define a custome color range between the minimal and maximal link identity:
MinLink Color
MidLink Color
MaxLink Color
Link opacity:
draw links ordered by identity
Set labels:
Label color
Label size:
Label color
Label size:
Label frequency:
size:
rotation:
offset: