I assume there are several options you can try. Some of them are as follows

1.https://sanger-pathogens.github.io/Roary/

2.http://pangp.big.ac.cn/

3.http://cge.cbs.dtu.dk/services/PanFunPro/

4.https://lfz.corefacility.ca/panseq/analyses/

5.https://www.researchgate.net/deref/https%3A%2F%2Fedgar.computational.bio.uni-giessen.de%2Fcgi-bin%2Fedgar_login.cgi

6.https://github.com/eead-csic-compbio/get_homologues

After genome assembly, you can:

1) Extract 16S rRNA genes and construct a phylogenetic tree

2) Use Whole genome sequences to construct phylogenetic tree (e.g. PhyloPhlAn software)

I suggest you two different tools:

1) Roary (https://sanger-pathogens.github.io/Roary/). You can use this to build a phylogenetic tree with core genes.

2) UBCG (https://help.ezbiocloud.net/ubcg-users-manual/) with this tool you can use 92 housekeeping genes to build a very nice phylogenetic tree

Thank you everyone for suggesting various tools. I highly appreciate your help.