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Bacterial Synteny Tools

Hi,

I'm trying to generate some synteny plots for >10 whole bacterial genomes can anyone suggest some tools? These genomes are ~2.3 mb and contain a lot of rearrangment and repeats.

Cheers

comparative bacteria synteny
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updated by Will • Will • written by John • John

3 answers

Hello,

I have used TBtools to make multiple syntenys (https://github.com/CJ-Chen/TBtools-II) and for more attractive visualization I have used SynVisio (https://synvisio.github.io/#/)

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written by san96 • san96

some possible tools

progressiveMauve gggenomes gggenes genoplotR pyGenomeViz clinker plotsr

from looking at https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Comparative

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written by cmdcolin cmdcolin

clinker and sibeliaX are the best IMO.

Sibelia in particular is designed for exactly this task and can even produce plots of all vs all comparisons, which most other tools won't.

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written by Joe Joe

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