If you want to use the blast result for making the phylogenetic tree. First you reterive the sequences of high similarity sequences then perform multiple sequence alignment and by this you can easily make the phylogenetic tree.
First you retrieve sequences of high similarities using blast. Then use these sequences in clustalW to genrate a phylogenetic tree. Use treeview to view this phlogenetic tree.
Best method is. select 2-4 top blast sequences from every organism and DO multiple sequence allignment, and make tree.
Software you can use:
Jalview
MEGA
Few online tools.
http://www.phylogeny.fr/version2_cgi/simple_phylogeny.cgi
(one click server)
http://www.phylogeny.fr/version2_cgi/advanced.cgi
(with advanced options)
List of tools:
http://molbiol-tools.ca/Phylogeny.htm
u can use any phylogenetic software like MEGA and choose N-J method for generating phylogenetic tree.
Hi Dushyant,
if you are starting with the unknown query sequence, I would suggest you to do the BLAST in the Ref sequence database and then you can select the appropriate sequences on the basis of E value and query coverage. The other method which is even easier, is creating the phylogenetic tree in the BLAST result interface itself, which will generate (.dnd) file. You can view that in TREEVIEW or similar one. If you are selecting the homologous sequences manually, then i would suggest you to use CLUSTALX to generate phylogenetic map (.dnd file) and view in above mentioned software.
I would also prefer MEGA, it will also export your result in a easy way.
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