Hi Manal, The XMFA format nucleotide alignment is in the "base" file name that you would have specified in the GUI when constructing the alignment with progressiveMauve. If you used the command-line, it's the filename provided in the --output= option. Mauve doesn't compute consensus sequences, but you might be able to do this with some scripting or a 3rd party program.
On Sat, 2013-08-31 at 00:22 +1000, Manal Farid wrote: > how could I view the aligned sequence (to get consensus sequence) > after aligning a reference strain with a file containing assembled > scaffolds. > > which file should I use to viw the alignment (in the form of > nucleotides) not LCBs > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
