Hi Zhao, It's difficult to predict progressiveMauve's runtime because it depends on a number of factors including the degree of divergence in the genomes you are aligning and the quality with which they have been assembled.
One thing is certain, though, which is that the current version of progressiveMauve is going to need much more than 4GB RAM to align a set of 50 genomes each 6MBp. I would expect it to use 30GB if not more. Best, -Aaron On Thu, 2013-10-10 at 13:11 +1100, Zhao Jin wrote: > Dear list, > > > I am trying to use Mauve 2.3.1 to find core- and pan- > bacterial genomes, so I wonder how long it would take to align 48 > bacterial genomes, ~ 6 MB each, on a 64-bit Linux with 4 GB memory > using the progressive aligner and recursive anchor search and looking > for LCBs. > > > Thank you, > Zhao > > > -- > Zhao JIN > Ph.D. Candidate > Ruth Ley Lab > 467 Biotech > Field of Microbiology, Cornell University > Lab: 607.255.4954 > Cell: 412.889.3675 > -- 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. ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
