Phylogenetic tree for 16s sequences in a metagenomic data set

Question

[surathsanda]

I have about 350 fasta sequences (16s) of gut bacteria. I want to make phylogenetic tree. I am new to this field, There are some de novo sequences they are different but blast will show it is same species. i want to know to make the phylogenetic tree, do i need to add all the sequences that blast to same species, and if not how can i select one of the sequences. and also what are the tools i can use. I only know mega software.