Hi Susan, On Tue, 2015-12-08 at 20:05 +0000, Susan Beth Fogelson wrote: > Thank you for all of your helpful responses. I guess at this point my > question changes. I would like to build a phylogenetic tree of this > alignment and I assume I need to convert the XMFA file to another > format to complete this task. Has anyone had experience with file > conversion and what program would you recommend for phylogenetic tree > reconstruction? At present I am using MEGA6 but I think these files > are too big for that program to run effectively.
There are many ways to build phylogenies from Mauve alignments and hopefully others on the list will chime in with suggestions. Once you have an initial tree, you might consider ClonalFrameML as a way to help reduce the impact of historical recombination events on tree inference: https://github.com/xavierdidelot/clonalframeml/wiki Best, -Aaron -- 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.
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