Aaron,
Could the guide tree be used to group samples within a serotype or would
that too be a misinterpretation?
-Amarin
On Tue, Dec 8, 2015 at 4:41 PM, Aaron Darling <aaron.darl...@uts.edu.au>
wrote:
> 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
>
>
>
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