OAT has a disadvantage of selecting only 10 strains. A large number will help in better understanding on inter-relationships.
Hello Aparna,
I think you'll be able to accomplish this with Bioconductor - not having done it myself, though.
Check out: https://bioconductor.org/packages/release/bioc/html/FindMyFriends.html
It states it can be used for making the pangenome matrices. Once you have the matrices, it should be relatively straightforward (assuming the matrices are not broken up in any peculiar way) to plot the heatmaps with any standard heatmap plotting functions in R. I personally really like the aheatmap() function in the NMF package.
Hope this helps.
Hello Aparna,
I believe MAuve does whole genome heatmap. Checkout this link http://darlinglab.org/mauve/mauve.html. I have not used it for such before but some publications have constructed heatmap using MAuve. Read more about the publication here: https://openi.nlm.nih.gov/detailedresult.php?img=PMC3539920_1471-2180-12-273-1&req=4
https://bioconductor.org/packages/3.7/bioc/vignettes/EnrichedHeatmap/inst/doc/EnrichedHeatmap.html
I m doing the same on Circos, very powerful tool: http://circos.ca/
Let me know if you encounter any trouble, could be intimidating on the beginning but I guess if you tried already another tool, should not be complicated.
Loubna
R system is difficult...! For Circos the interpretation and results are excellent! But running Circos in Windows based system is seems to be a little difficult.
I can not confirm that as I m working on Unix. Looking briefly on Circos s homepage, working on Windows should not cause any issue when using Cygwin as Bash shell and installing all needed perl modules.
Loubna
Aparna,
On windows to easily emulate linux (or unix) try MobaXTerm. It is free, very user friendly, and can quickly add plugins that are otherwise cumbersome to install like cygwin. If you try it and like it I highly recommend upgrading to the full version where you can get a permanent home folder and such - essentially converting a windows computer into a dual-boot system with a single program (that doesn't slow the windows side down).
https://mobaxterm.mobatek.net/
What kind of heat-maps do you want exactly? You mentioned OAT which is a tool to compare ANI of genomes, then I would recommend pyani as this tool can compare hundreds of genomes (ANI) in one go with nice heatmaps drawn for you.
Here is the link to install the software (however it runs on Linux system, a Python-based tool):
https://github.com/widdowquinn/pyani
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