Dear Xiangchen, I don’t know whether you can specify the number of iterations, but I don’t think you need to. The process proceeds through new alignments for as long as it can, and intermediate results are generated and available for you to view, so you can always check earlier results. In my experience, the process sometimes takes very few iterations (2-3) and sometimes more than 20, depending on the number of contigs and what order/orientation they were in initially. This has no bearing on the quality of the final ordering. Links below to additional documentation.
From the paper - http://bioinformatics.oxfordjournals.org/content/25/16/2071.full "Mauve assumes contigs are in the correct order when filtering matches, so as the order is optimized, alignment results change. Therefore, results are refined through iterative alignment until no further ordering is possible." Darling Lab site - http://darlinglab.org/mauve/user-guide/reordering.html Take care, Mark ------------------------------ Mark J. Mandel, Ph.D. Assistant Professor Department of Microbiology-Immunology Northwestern University Feinberg School of Medicine 320 E. Superior St., Searle 3-403 Chicago, IL 60611 m-man...@northwestern.edu<mailto:m-man...@northwestern.edu> http://labs.feinberg.northwestern.edu/mandel/ (312) 503-4138 Office (312) 503-2915 Lab (312) 503-9594 Fax On Nov 3, 2015, at 8:31 PM, lixiangche...@outlook.com<mailto:lixiangche...@outlook.com> wrote: Hi, Currently I am using "Mauve contig mover" to make an ordering of contig. I find only 15 alignments in the result. I think the final alignment should be the best. I think the more the iterations is, the more accurate the reodering is. So can I change the default number of alignments in the reordering process? Best, Xiangchen ________________________________ lixiangche...@outlook.com<mailto:lixiangche...@outlook.com> ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net<mailto:Mauve-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/mauve-users
------------------------------------------------------------------------------
_______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
