Re: [Mauve-users] Calculating a "real" whle genome pyhlogenetic tree using mauveAligner

[Aaron D. <aar...@ut...>]

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, mic...@ag...
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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