Tool for phylogenetic tree creation of Genome

Question

[microorganism_001]

I want to create a phylogenetic tree of a few genomes of bacteria but I am facing a problem of not getting a suitable tool. Can anyone suggest the best tool for this purpose? I have a system of 32GB RAM. I used MEGA tool but there is one problem I am facing because the genome belongs to different lengths. Thanks.

[GenoMax]

Past threads that should help:

Which alignment for whole bacterial genomes for phylogenetic tree?
phylogenetic tree construction using scaffolds of genome against specific gene of interest
Phylogenetic tree from denovo assemblies