How indentify shared genes between two or more bacterial genomes?

Question

[ayixon]

I need two compare 5 distant bacterial genomes looking for shared genes. Can anyone suggest a tool?

[Sishuo Wang]

You might want to have a look at link.

Answer 1

[Fabio Marroni]

Mummer. Just because is the only one I know!

Answer 2

[Carambakaracho]

try aligning Diamond alignments of all proteins of one genome against all proteins of another genome and repeat this until you get all to all comparisons. Choose the output format you like best and define a suitable threshold on for example identity or use something like reciprocal-best blast hits (see the good old COG software) to find orthologous/paralogous clusters. See also the EggNOG methods