I recommend MEGAN, but it require annotated file (can be created using Blastx against NR database) of genes in your genomic data, It is best automated tool to find not only phylogeny but also give other annotation comparison like GO, KEGG and SEED. this tool usually for metagenomic data analysis.
Alternatively you can try ROARY (https://github.com/sanger-pathogens/Roary) & REALPHY (Reference sequence Alignment-based Phylogeny builder).
You should also read this thread which is identical:
https://www.researchgate.net/post/How_do_I_construct_a_phylogenetic_SNP_tree_using_whole_genome_sequences_of_bacteria2
Good Luck!
I recommend MG -RAST http://www.ncbi.nlm.nih.gov/pubmed/22515215 working excellently for more than 6 years, and with updated functions at: http://nar.oxfordjournals.org/content/early/2015/12/09/nar.gkv1322.full
Have you tried WOMBAC?
http://www.vicbioinformatics.com/software.wombac.shtml
Wombac rapidly finds core genome SNPs from samples and produces an alignment of those SNPs which can be used to build a phylogenomic tree. It can handle 100s of samples and uses multiple CPUs on a single system efficiently. Computations can re-used for building new trees when new samples are added, saving lots of time. Wombac only looks for substitution SNPs, not indels, and it may miss some SNPs, but it will find enough to build high-resolution trees.
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