Re: [Mauve-users] Calculating a "real" whle genome pyhlogenetic tree using mauveAligner
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koadman
From: Aaron D. <aar...@ut...> - 2016-10-04 13:40:21
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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 > > ------------------------------------------------------------------- > ----------- > _______________________________________________ > Mauve-users mailing list > Mau...@li... > 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. |