I can imagine there would be consistency between guide tree groups and
serotype in some or even most cases but, if you want to group by
serotype I am not sure the guide tree is a good proxy. But I know little
about serotypes and how they work in various organisms.
On Tue, 2016-01-19 at 10:02 -0500, Amarin Cogburn wrote:
> 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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--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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