Hi Dag, On Mon, 2009-10-26 at 15:49 +0100, Dag Anders Brede wrote: > Hi, > > I hope that someone can help me, because I'm experiencing difficulties with > the following feature in the mauve 2.3.0: > > "Export a file containing alignments of orthologous CDS, including alignments > of unannotated regions predicted to be > orthologous" > > I can not find any description of this application in the user guide. Is > there a step by step description for use in the command line window?
You are correct that the user's guide does not contain a description of the export orthologs functionality. It is not currently possible to invoke the ortholog export functionality from a command-prompt, it is a GUI-only feature implemented in Java. If you need that feature accessible via command-line immediately and have expertise with Java development, I would be happy to provide advice on how to implement it. I have just added a description of the ortholog export file format to the User's Guide, see this page: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html A description of the algorithm used by Mauve to predict positional orthologs based on whole-genome multiple alignments is forthcoming. Once finished it will appear in the user's guide as well. Cheers, -Aaron ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
