One of our collaborators lab recently isolated virus samples from patients. I received the sequenced reads from MiSeq for those virus samples. Then I investigated the SNVs present in the samples. Now I am interested in creating a phylogenetic tree for Neuraminidase gene with the other NA sequence in the GenBank database. Therefore, I would like to know
1) how to generate FASTA sequence of the NA gene from the MiSeq sequenced reads?
2) What are the factors to be considered while generating a phylogenetic tree for viruses? because viruses mutates at a much faster rate compared to prokaryotes.
3) Any tools recommended for performing the phylogenetic tree.
Thanks in advance.