What is the best method to compare the evolution of a single pathway within different species with the evolution of the entire genomes?

03 March 2014 1 451 Report

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?

Pieter Stragier

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?

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Science method

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