I have a library of bacterial species that I identified via 16S rRNA sequencing and I'd like to make a fairly simple bacterial phylogenetic tree with all the major orders, so that I can annotate it with the grouping and number of species that I have identified. Is there a way to do this without manually gathering a representative 16S sequence for each order and doing the trees myself?
Hi
1. BLAST the FASTA files in NCBI ( BLASTn)
2. Find the most similar sequences. Save the FASTA format of the similar sequences.
3. Do it for all your sequences.
4. There are free Softwares like MEGA5 or BioEDIT where you can easily align the sequences and construct a phylogenetic tree as per your wish.
If your library is too large you may try it with RDP classifier ( Ribosomal database Project, online only). But you may need some programming to run all your data at a time in RDP classifier.
Thanks for your reply Jyotsnarani, however I don't want to actually make a tree of all of my sequences. I'd like to show their location on a broader tree of the bacterial orders, so I can give an indication of the groups of bacteria that were present. I could just take a tree from google and add my species to it but I don't think that's really acceptable!
the tool ARB provides databases to add what ever you like and even to adjust and calculate those things.
Visit http://tolweb.org/tree/. You might even like to contribute.
MEGA 5 is the easiest and quickest for a simple tree. However, ARB is a great program once you are comfortable with the operations
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