Hi there :)
My colleague is asked by his boss to construct phylogenetic trees based on each gene in the genome of a new bacterium that was sequenced in our lab. One simple way to do that, my colleague believes, is to blast for similar sequences from genbank for each gene in the genome, build a multiple alignment from this similar sequences for each gene, and construct a tree for each gene. The problem is that the genome has around 2,000 genes in it. So we wonder if there is a way to automate this process.
I myself don't really understand why my colleague's boss wants to have those trees, but my colleague told me that they would like to know the exact phylogenetic position of this new bacterium. Do you think it is a wise way to do that? I mean, I don't understand what they can tell at the end if they have 2,000 phylogenetic trees that might not have similar topologies to one another. I thought about consensus tree, but what if there are different organisms from one tree to the other? Or does he want to find lateral gene transfers?
So please if you have any idea, comments or experience with these kinds of problems, we would be really grateful to hear from you, especially about the tree construction part (it's what my colleague's boss asked for anyway).