Hi Bhav, A handful of things changed in the implementation of library functions during the development of progressiveMauve (the main new feature in the 2.x release series) that also changed mauveAligner (because they use some of the same library functions). I don't have a summary of the details of how the changes affected mauveAligner, but all changes are in the source code revision history if you are interested in the guts. For the purpose of finding islands I would very strongly suggest considering progressiveMauve for this task, since mauveAligner can only align "core" regions of the genome and in any sizeable collection of genomes there will be many "almost core" regions that it would miss.
Best, -Aaron On Wed, 2014-07-30 at 14:22 +1000, Bhavjinder Dhillon wrote: > Hi, > > I'm wondering if anything has changed between versions 1 and 2 for the > mauveAligner algorithm? I'm updating some software that used > mauveAligner v1.2.3 to identify islands and I'm noticing that v2.3.1 > produces a handful more islands. Is this because the alignment was > different/better? I was under the impression that the new and improved > alignment algorithm was implemented under progressiveMauve and that > mauveAligner was the same as previous versions. It would be really > helpful if you could confirm that these differences are expected and > are improvements from the older version and not the result of > something I may be misinterpreting. > > Thank you, > Bhav > > -- > Bhavjinder Kaur Dhillon > CIHR/MSFHR Bioinformatics PhD Candidate > Brinkman Laboratory, MBB Department > Simon Fraser University, Burnaby BC, Canada, V5A 1S6 > Phone: 778-782-5414 Fax: 778-782-5583 > > -- 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. ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
