Hi Max, On Wed, 2015-10-14 at 20:45 +0000, Tagliamonte,Massimiliano S wrote:
> would like to use the resulting files for phylogenetic analyses. I am > interested in the snapshots xmfa2maf and stripsubsetLCB. I am not sure > I have a clear idea of what they do, how to use them or which folder > they should be placed in order to work. Can they be called from the > GUI or are they command line only? These are command-line only programs. The ClonalOrigin page contains an example of using stripSubsetLCBs in the context of another workflow: https://github.com/xavierdidelot/ClonalOrigin/wiki/Usage I'm afraid there is not really any further documentation on stripSubsetLCBs at this stage. > I failed to find a manual regarding the snapshots, is there a link > to it? Do you mean stripSubsetLCBs / xmfa2maf snapshots? Or the Mauve snapshots? You probably already found the Mauve manual here: http://darlinglab.org/mauve/user-guide/introduction.html Best, -Aaron
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