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.sch...@agroscope.admin.ch
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
>
> -------------------------------------------------------------------
> -----------
> _______________________________________________
> Mauve-users mailing list
> Mauve-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mauve-users
--
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.
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
