Hi Aaron,
Would this be also a good option for > 100 genomes?
On Tue, Oct 4, 2016 at 4:39 PM, Aaron Darling <aaron.darl...@uts.edu.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.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
> listMauve-users@lists.sourceforge.nethttps://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
>
>
------------------------------------------------------------------------------
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
