Can raxml-ng output the distance matrix of my sequences

[彭业博]

Hello everyone,

I want to get the distance matrix of my sequences, but I didn't find any parameter to do that. 

Can raxml-ng do that?

yebo

[Alexandros Stamatakis]

Hi Yebo,

As far as I know, RAxML-NG can't do this, but there is an option in good
old standard RAxML (see manual at:
https://cme.h-its.org/exelixis/resource/download/NewManual.pdf) that can
do it.

Alexis

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Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[彭业博]

Hi Alexis,

Thank you! 

I actually want to make the heatmap plot after the tree have been built. So, may I compute the pairwise distance from the phylogenetic tree (using its branch lengths)? Do you believe it's an alternative way?

Best,

Yebo

Alexandros Stamatakis <alexandros...@gmail.com> 于2021年3月24日周三 上午2:28写道：

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[Alexandros Stamatakis]

Hi Yebo,

> Thank you!
> I actually want to make the heatmap plot after the tree have been built.
> So, may I compute the pairwise distance from the phylogenetic tree
> (using its branch lengths)? Do you believe it's an alternative way?

Yes that's a good way (I guess you mean the patristic distances?) if you
want to base that heatmap on the phylogenetic inferences you conducted
anyway.

That's surely more consistent.

Alexis

>
> Best,
> Yebo
>
> Alexandros Stamatakis <alexandros...@gmail.com

> <mailto:alexandros...@gmail.com>> 于2021年3月24日周三 上午2:28写道：

>
> Hi Yebo,
>
> As far as I know, RAxML-NG can't do this, but there is an option in
> good
> old standard RAxML (see manual at:
> https://cme.h-its.org/exelixis/resource/download/NewManual.pdf

> <https://cme.h-its.org/exelixis/resource/download/NewManual.pdf>)

> that can
> do it.
>
> Alexis
>
> On 23.03.21 16:15, 彭业博 wrote:
> > Hello everyone,
> >
> > I want to get the distance matrix of my sequences, but I didn't
> find any
> > parameter to do that.
> > Can raxml-ng do that?
> >
> > yebo
> >
> > --
> > 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%2Bunsu...@googlegroups.com>
> > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.

> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/raxml/b93dcc82-2d40-4142-b0c3-f94a6977a66bn%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/b93dcc82-2d40-4142-b0c3-f94a6977a66bn%40googlegroups.com>
>
> >

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>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

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

>
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