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林子熙

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Jun 6, 2023, 9:14:26 AM6/6/23

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Dear all,

I generated an evolutionary tree with raxml, but the root of the tree does not show the support rate, I think the support rate below 50 does not show, so how do I show the support below 50 at the root.

Xu jun

Alexandros Stamatakis

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Jun 6, 2023, 11:48:40 AM6/6/23

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This seems to be a tree visualization issue, maybe you want to share the
tree you want to visualize.

Alexis

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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

林子熙

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Jun 6, 2023, 9:41:03 PM6/6/23

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Alexandros Stamatakis

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Jun 7, 2023, 10:18:45 AM6/7/23

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The rooting via an outgroup is just a drawing option, internally the
tree is being treated as unrooted tree, hence there is no support at the
node that is the pseudo-root for drawing the tree.

If you think of this tree as being unrooted by removing the root, all
support values are there actually.

If you want to obtain statistical support values for different root
placements on the ingroup tree, you may want to use RootDigger instead:

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-03956-5

Alexis

On 07.06.23 04:41, 林子熙 wrote:
> 2a4827a0455c32e9967fc95455acb8e.png
>
> 在2023年6月6日星期二 UTC+8 23:48:40<Alexandros Stamatakis> 写道：
>
> This seems to be a tree visualization issue, maybe you want to share
> the
> tree you want to visualize.
>
> Alexis
>
> On 06.06.23 16:14, 林子熙 wrote:
> > Dear all,
> >
> > I generated an evolutionary tree with raxml, but the root of the
> tree
> > does not show the support rate, I think the support rate below 50
> does
> > not show, so how do I show the support below 50 at the root.
> >
> > Xu jun
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com
> > <mailto:raxml+un...@googlegroups.com>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/raxml/52a5a3a9-561d-45c2-b2a8-380ebb8d6401n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/52a5a3a9-561d-45c2-b2a8-380ebb8d6401n%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/52a5a3a9-561d-45c2-b2a8-380ebb8d6401n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/52a5a3a9-561d-45c2-b2a8-380ebb8d6401n%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>
> --
> Alexandros (Alexis) Stamatakis
>
> ERA Chair, Institute of Computer Science, Foundation for Research and
> Technology - Hellas
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

> www.biocomp.gr <http://www.biocomp.gr> (Crete lab)
> www.exelixis-lab.org <http://www.exelixis-lab.org> (Heidelberg lab)

>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/760dc87f-735a-4c12-becf-4b2e43f51390n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/760dc87f-735a-4c12-becf-4b2e43f51390n%40googlegroups.com?utm_medium=email&utm_source=footer>.

林子熙

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Jun 7, 2023, 10:08:12 PM6/7/23

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We build rooted trees, not rootless trees, unless the software doesn't build based on the roots.

Xu Jun

Alexandros Stamatakis

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Jun 8, 2023, 1:51:54 AM6/8/23

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could you share the command lines you used for the inferences?

Alexis

On 08.06.23 05:08, 林子熙 wrote:
> We build rooted trees, not rootless trees, unless the software doesn't
> build based on the roots.
>
> Xu Jun
>
> 在2023年6月7日星期三 UTC+8 22:18:45<Alexandros Stamatakis> 写道：
>
> The rooting via an outgroup is just a drawing option, internally the
> tree is being treated as unrooted tree, hence there is no support at
> the
> node that is the pseudo-root for drawing the tree.
>
> If you think of this tree as being unrooted by removing the root, all
> support values are there actually.
>
> If you want to obtain statistical support values for different root
> placements on the ingroup tree, you may want to use RootDigger instead:
>

> https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-03956-5 <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-03956-5>

>
> Alexis
>
> On 07.06.23 04:41, 林子熙 wrote:
> > 2a4827a0455c32e9967fc95455acb8e.png
> >
> > 在2023年6月6日星期二 UTC+8 23:48:40<Alexandros Stamatakis> 写道：
> >
> > This seems to be a tree visualization issue, maybe you want to share
> > the
> > tree you want to visualize.
> >
> > Alexis
> >
> > On 06.06.23 16:14, 林子熙 wrote:
> > > Dear all,
> > >
> > > I generated an evolutionary tree with raxml, but the root of the
> > tree
> > > does not show the support rate, I think the support rate below 50
> > does
> > > not show, so how do I show the support below 50 at the root.
> > >
> > > Xu jun
> > >
> > > --
> > > You received this message because you are subscribed to the Google
> > > Groups "raxml" group.
> > > To unsubscribe from this group and stop receiving emails from it,
> > send
> > > an email to raxml+un...@googlegroups.com
> > > <mailto:raxml+un...@googlegroups.com>.
> > > To view this discussion on the web visit
> > >
> >

> >
> > --
> > Alexandros (Alexis) Stamatakis
> >
> > ERA Chair, Institute of Computer Science, Foundation for Research
> and
> > Technology - Hellas
> > Research Group Leader, Heidelberg Institute for Theoretical Studies
> > Full Professor, Dept. of Informatics, Karlsruhe Institute of
> Technology
> >

> > www.biocomp.gr <http://www.biocomp.gr> <http://www.biocomp.gr

> <http://www.biocomp.gr>> (Crete lab)
> > www.exelixis-lab.org <http://www.exelixis-lab.org>

> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>

> (Heidelberg lab)
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com
> > <mailto:raxml+un...@googlegroups.com>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/raxml/760dc87f-735a-4c12-becf-4b2e43f51390n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/760dc87f-735a-4c12-becf-4b2e43f51390n%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/760dc87f-735a-4c12-becf-4b2e43f51390n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/760dc87f-735a-4c12-becf-4b2e43f51390n%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>
> --
> Alexandros (Alexis) Stamatakis
>
> ERA Chair, Institute of Computer Science, Foundation for Research and
> Technology - Hellas
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

> www.biocomp.gr <http://www.biocomp.gr> (Crete lab)
> www.exelixis-lab.org <http://www.exelixis-lab.org> (Heidelberg lab)
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/2cccf306-c7e2-44f4-b952-87266b5698cdn%40googlegroups.com <https://groups.google.com/d/msgid/raxml/2cccf306-c7e2-44f4-b952-87266b5698cdn%40googlegroups.com?utm_medium=email&utm_source=footer>.

林子熙

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Jun 8, 2023, 9:34:25 PM6/8/23

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./raxml-ng --all --msa COX_ND.fas --outgroup KT005800.1_japonicus --model mtDNApartition.txt --model GTR+G --tree pars{10} --bs-trees 1000

Xu Jun

Grimm

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Jun 9, 2023, 3:10:18 AM6/9/23

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Hi Jun,

that command line, which invokes the default tree inference, gives you an unrooted tree. You only infer explicitely rooted trees, when using an asymmetric model (e.g. binary Dollo, only change possible is from 0 -> 1). Any GTR+Gamma model implementation always leads to an unrooted tree. The "outgroup" option only roots the inferred unrooted tree by assuming KT005800 is the outgroup (the graphic manipulation, Alexi mentioned), i.e. places the root on the KT005800 terminal branch.

Which is what we call a trivial split: KT005800 | all other tips. It's called a "trivial split" because any terminal internode, the connection between a tip and the rest of the tree, must be in all bootstrap pseudoreplicates, it's BS support is always 100. Only the internodes seperating two or more tips from all others, i.e. the splits that divide the taxon set into two subset, hence, also called taxon bipartitions, are optimised and gauged during tree inference. Note that to establish BS support, we simply count the biparitions across the pseudoreplicate tree samples.

FigTree, being designed for dated trees, which are ultrametrised, hence, have an implicit root without the need to define an outgroup, interpretes the internode support as the support for the next higher node in the (here) outgroup-rooted tree. Here's a quick to the point for your tree.

But BS support are always branch support (internode) values, never node supports (common error in phylogenetic literature): a node in a tree is the joining point of tree internodes, i.e. depedending where I place the root, I propagate the support of one of the three internodes on the connecting node when viewing a standard NEWICK tree in (most) tree viewer(s) and assuming one or several tips represent the sister lineage, the outgroup. Placing BS support on nodes is an interpretation, not a result. PS this is also the reason why FigTree allows you to view the branch support on branches as the primary result (click-down menu: branch labels). BTW, the same holds for posterior probabilities, they are also inferred branch support, not node support!

The critical bipartition regarding the deep relationships in your data set is the violet split with the ambiguous BS support of 57: outtaxon tip + blue species | remaining ingroup. Noting the extreme phylogenetic distance (i.e. via the tree's branches) between all of the ingroup and the (single-tip) outgroup compared to the phylogenetic distance between the three "species" groups (could be populations, but genetically they would be species being high-coherent; here near-invariable); the low support for this critical bipartition (or internode, or branch) could be due to ingroup-outgroup long-branch attraction: ML has a 50% chance to escape LBA in the so-called Felsenstein Zone, and it well may be that it's 57 to 43 for the LBA-triggered purple split vs. a non-LBA biased alternative. Or it may be that some BS pseudoreplicate dataset suffer less from ingroup-outgroup LBA than others. Or that it is the genuine root, and the greens are sisters to the rest, but some BS pseudoreplicates (the other 43%) suffer from LBA.

You can visualise the alternative in the BS pseudoreplicate sample by reading in RAxML's bootstrap sample into e.g. SplitsTree or using the Networx object implemented in R/phangorn.

See this open access paper:

Schliep K, Potts AJ, Morrison DA, Grimm GW. 2017. Intertwining phylogenetic trees and networks. Methods in Ecology and Evolution 8:1212–1220. http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12760/full

Cheers, Guido.

Grimm

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Jun 9, 2023, 3:18:39 AM6/9/23

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Re the " support rate below 50 does not show "; by default FigTree shows all supports irrespective of their amplitude. Here's a RAxML output tree (from classic RAxML) opened properly with FigTree (branch labels ticked for bootstrap, not node labels).

(but see Czech L, Huerta-Cepas J, Stamatakis A. 2017. A critical review on the use of support values in tree viewers and bioinformatics toolkits. Molecular Biology & Evolution 34:1535–1542. https://doi.org/10.1093/molbev/msx055)

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