For a certain bacterial pathway I conducted some evolutionary analyses. Now, I would like to compare this evolutionary model with the evolutionary model of the entire genomes. How can I do this? What is the best way to analyze the evolution of a pathway within different species? Which tools are up for this task?
I ran orthoMCL and ITEP. But I'm not satisfied yet. I wish to obtain a species tree based on the orthoMCL results and the core genes, to compare this tree with the species/pathway tree of all my species. This way I could predict HGT. But I'm stuck. I suppose I could run all this with different tools, but 1) I wondered if there is one tool that could do it all and 2) what analysis should I run in the first place that are better than orthoMCL?
I'm a little confused about what you're looking for-- are you just trying to compare gene or "pathway" trees to species trees, or are you interested in looking for evidence of convergent evolution along distinct lineages, or are you interested in looking for different kinds of selection (ie, purifying, neutral, positive), or....?
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