I just finished sequencing my samples. Of the 11 samples, 7 isolates showed decent results after further analysis using SeqTrace. Afterwards, the sequences were uploaded to BLASTX to make sure that the sequences were actually the targeted gene (rocF gene, which encodes arginase). From the 7 isolates, 4 of them show 78-93% similarity to the arginase from the bacteria Halalkalibacterium halodurans, whereas the other 3 show 95-98% similarity to Bacillus safensis & Bacillus tequilensis. Now, I am going to do a phylogenetic analysis on these 7 bacterial isolate sequences. How can I determine which reference sequences to use? Do they need to contain the arginase sequence or can they be randomly picked as long as they are from the same genus? Do I also need to include the outgroup? If yes, what outgroup can I use in this phylogenetic tree construction? Thanks
Hi Agnes, you don't necessarily need other sequences, you can just align yours to each other (use clustal omega for example) and create a tree (probably unrooted). if you want an outgroup pick something relatively closely related but definitely outside Halalkaibacterium and Bacillus (I don't work on bacteria, so I can't advise specifics). But you need the same gene to be available, not a random gene.
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