how to analyze synteny between 4 genomes. please suggest suitable tool

Question

[kaurjaimeet911]

i want to analyze synteny of 4 genomes .therefore it is my humble request to kindly suggest any suitable tool

[microfuge]

Synmap is a good tool but works only up to 3 genomes (https://genomevolution.org/coge/SynMap3D.pl)

[Sej Modha]

+1 for Synima, I have recently used to for multiple Plasmodium genomes and it worked like a charm!

Answer 1

[jean.elbers]

https://github.com/rhysf/Synima

Answer 2

[lieven.sterck]

i-ADHoRe is another option, rather for analyzing (or looking for synteny) then visualising though (can't make up from your question what the exact goal is?)

Answer 3

[Kevin Blighe]

You may find utility in these:

• Synteny Portal: a web-based application portal for synteny block analysis
• mySyntenyPortal: an application package to construct websites for synteny block analysis (just published)
• Genomicus (recommended by a colleague)

Kevin

Answer 4

[Joe]

I suggest Sibelia. It will draw you a circos plot of the synteny conservation. If you're only interested in specific gene regions/operons, try MultiGeneBlast.