Re: [Mauve-users] Calculating a "real" whle genome pyhlogenetic tree using mauveAligner
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From: Aaron D. <aar...@ut...> - 2016-10-07 11:50:30
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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, mic...@ag...min.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 > > > > > > --------------------------------------------------------------- > > > --------------- > > > _______________________________________________ > > > 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. > > > > ----------------------------------------------------------------- > > ------------- > > 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 > > Mau...@li... > > 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 > 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. |