Dear Aaron,
Thanks for your kind answer. I was looking for at least a brief explanation of the function and parameters of stripSubsetLCBs / xmfa2maf snapshots. As I have a biology background, writing my own scripts is still a very time expensive step for me. The link you provided helps a lot for the stripSubset, while the xmfa2maf should be pretty straight forward. I'll try them and see how it goes :) Regards, Max Massimiliano S. Tagliamonte Graduate Student University of Florida College of Veterinary Medicine Department of Infectious Diseases and Pathology From: Aaron Darling <darl...@cs.wisc.edu> Sent: Wednesday, October 14, 2015 7:45 PM To: mauve-users@lists.sourceforge.net Subject: Re: [Mauve-users] Mauve snapshots usage in Windows 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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