How do we select the best outgroup for constructing phylogenetic tree? Suppose if my isolate is gram positive. Can I select the outgroup from gram negative group.
Depends on what your study is trying to address.
For example, if you're trying to compare your species with other gram-positve species, and trying to highlight similarities in Gram-positive species compared to gram-negative. Or highlight differences between gram-positive to gram negative. Then using a gram-negative bacteria makes sense.
if you're trying to show how unique or different your bacteria is, then it would make more sense to compare it to other close species that are gram-positive.
Thanks for your suggestion.
I have one more question.
Can i compare 3-4 species of bacteria only without selecting any outgroup. Is it the right way of presenting phylogenetic analysis.
A minimum tree to infer any information is 3 branches, and frankly I doubt with 3-4 species any useful information could be inferred. At this age where lots of sequence information is available, using only 3-4 species only, I would say is highly unusual practice.
You can do a tree without outgroup (I would highly suggest with more species), but again it depends on what you want to infer from the tree.
I would strongly suggest you to read up more on phylogenetic trees structure, outgroups, and how to present information with the tree. Here are some basics
http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo2a.htmlhttp://evolution.berkeley.edu/evolibrary/article/phylogenetics_01
whether the outgroup can be within same genera
Can I use a fungus as an outgroup for my Gram positive bacterial phylogenetic tree?
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