Hi, First off thanks for the great program. I am using it to align 30-50 very closely related genomes. ProgressiveMauve does a much better job at a fraction of the time than existing applications. But I am running into one small and I feel probably correctable error. Regions where a strain or two has a large (5-20kb) deletion relative to other strains the alignment gets slightly messed up. The aligner for some reason is introducing breaks in the alignment of other strains and failing to correctly align all of the strains within that region. I am assuming that there may be a gap penalty parameter that I could increase to prevent this. This leads to my question, what are the defaults for the gap penalty parameters of progressiveMauve? I don't even know what value to start with for most of the parameters. Since I know where most of the large insertions are, introducing hardmasked sequence at the site seems to alleviate the problem. But I feel this is kind of hack on my part and tuning the aligner to correctly perform the alignment would be ideal.
Best, Ryan ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
