Are there any software for the alignment-free bacterial whole genome sequence similarity search and comparison?

Question

[hrenchert747]

Are there any working software (s) for the alignment-free bacterial whole genome sequence similarity search and comparison? Thx.

Answer 1

[kloetzl]

If all you want is a tree via evolutionary distances, there are plenty of tools available:

• andi (shameless self-plug ☺)
• spaced words
• mash
• co-phylog
• kr, alfred, missmax, aff, csc, skrakov-phy, …