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Mauve uses a fast sequence matching algorithm to identify Locally Collinear Blocks (LCBs) between genomes. It has a really slick interface for viewing whole genome alignments or of viewing your genome assembly aligned to a closely related species.
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Install Mauve
On your Desktop (local) machine. Go here in a web browser:
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Choose Linux (it's ok to leave the other boxes blank).
Mauve has a binary that you should be able to launch by double-clicking on it.
Download Data
In a terminal on your Desktop (local) machine.
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