Best tools for pan genome analysis?

Question

[Alec Watanabe]

Hi, I'm working with more than a 100 bacterial genomes of Proteus and want to do a pan genome analysis of the genus. I'm currently using Prokka to annotate genomes which were downloaded from the NCBI and Roary will be used for the pan genome analyses. I want to know if:

1. these softwares are reliable for pan genome analyses;
2. if they are up-to-date;
3. if you recommend any other tools for this purpose.

Please, keep in mind that I am working with a significant amount of genomes and thus webtools like PanWeb won't handle this much data.

Thanks!

[GenoMax]

Obligatory link from Omics tools while you wait for other answers.

Answer 1

[Joe]

Roary is written specifically for pangenome analysis, and is designed to take Prokka output

Answer 2

[Alec Watanabe]

Just to update this post for anyone who might come across this post.

I'm currently using GET_HOMOLOGUES for pan genome analysis, but mainly for core genome analysis. The graphical output is good and the software can produce ANI and AAI graphs.