Hi Shlomo,
The short answer is probably not, because progressiveMauve is unlikely
to scale to > 100 bacterial genomes. Might be ok for small viruses.
You might try the harvest tools by Todd Treangen & colleagues:
http://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html
It computes only a core genome alignment but that may be enough to
extract the phylogenetic signal of interest.
There are a range of read-mapping to reference genome based approaches
but I won't comment on those here.
Best,
-Aaron
On Wed, 2016-10-05 at 13:21 +0300, Shlomo Blum wrote:
> Hi Aaron,
>
> Would this be also a good option for > 100 genomes?
>
>
> On Tue, Oct 4, 2016 at 4:39 PM, Aaron Darling
> au> wrote:
> > Hi Michael, I realize this is coming late, but still want to post a
> > reply for the benefit of others who may be curious in the future.
> > There are a number of ways to generate phylogenies from genome
> > alignments. If you want to use Mauve I suggest doing the alignment
> > with progressiveMauve then extracting the core genome alignment
> > blocks with stripSubsetLCBs. From that point you could use
> > ClonalFrameML or another alternative. There are some example
> > instructions for these steps (and beyond that) on this page:
> > https://github.com/xavierdidelot/ClonalOrigin/wiki/Usage
> >
> >
> > On Fri, 2016-08-19 at 08:27 +0000, michael.schmid@agroscope.admin.c
> > h wrote:
> > > I am looking for a way to generate a phylogenetic tree of 30
> > > pseudomonas strains by using mauve. Since the guidetree outputted
> > > by progressiveMauve is not a "real" phylogenetic tree I am
> > > looking for another "whole genome approach".
> > >
> > > Would it be an option to generate a phylogenetic tree the
> > > following way?:
> > > 1. Get FastA file form 30 strains and concatenate into one file
> > > 2. Align them with command: mauveAligner --output=ps.mauve.phylip
> > > --output-alignment=ps.alignment.phylip --weight=300 --alignment-
> > > output-format=phylip --alignment-output-dir=. ../
> > > inp/all/all.fasta
> > > 3. Use raxml or fastree on the phylip which gets generated by
> > > mauveAligner
> > >
> > > Thx
> > > Michael
> > >
> > > ---------------------------------------------------------------
> > > ---------------
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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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--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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