Calculating IC Scores with Partial Gene Trees

[William Gearty]

Hi all,

I'm trying to calculate IC/ICA scores with some partial gene trees (as described here), but I ran into a problem.

I tried the following command:

 

raxmlHPC-AVX2 -m GTRGAMMA -L MRE -z Reeder_DNA_sp.phy.geneTrees.tre -n geneTreeMetrics

But it crashed after reading in the trees supplied by -z, with the error

ERROR: Cannot find tree species: Acrochordus_granulatus
The species names in the input tree and alignment file may not match, please check!
Assertion failed!

It seems (to me) that RAxML reads in the first tree, and then assumes that all of the following trees should have the same taxa?

Therefore, since this taxon is not in my first tree but is in my second tree, it crashes the program?

So, my question, does the first tree supplied by -z (at least for use with IC/ICA scores) always need to be a complete tree (i.e. with all taxa)?

Secondly, if I were to supply a tree (via -t, e.g. the best concatenated tree) and use the -f i option instead, would the first tree supplied by -z still need to be a complete tree?

Thanks in advance,

Will

--

William Gearty

PhD Student, Paleobiology

Department of Geological Sciences

Stanford School of Earth, Energy & Environmental Sciences

people.stanford.edu/wgearty

[Alexandros Stamatakis]

Dear Will,

> I'm trying to calculate IC/ICA scores with some partial gene trees (as

> described here <http://biorxiv.org/content/early/2015/07/06/022053>),

:-)

> but I ran into a problem.
> I tried the following command:
>
> raxmlHPC-AVX2 -m GTRGAMMA -L MRE -z Reeder_DNA_sp.phy.geneTrees.tre
> -n geneTreeMetrics
>
>
> But it crashed after reading in the trees supplied by -z, with the error
>
> ERROR: Cannot find tree species: Acrochordus_granulatus
> The species names in the input tree and alignment file may not
> match, please check!
> Assertion failed!
>
>
> It seems (to me) that RAxML reads in the first tree, and then assumes
> that all of the following trees should have the same taxa?
> Therefore, since this taxon is not in my first tree but is in my second
> tree, it crashes the program?
> So, my question, does the first tree supplied by -z (at least for use
> with IC/ICA scores) always need to be a complete tree (i.e. with all taxa)?

Yes, the tree passed via -z is assumed to be the species tree that
comprises all taxa, the trees passed via -t are the (partial) gene trees.

> Secondly, if I were to supply a tree (via -t, e.g. the best concatenated
> tree) and use the -f i option instead, would the first tree supplied by
> -z still need to be a complete tree?

Now I see, the only option that is actually supported for TC/IC score
calculations on partial gene trees is the one with -f i, that is, we can
not build a consensus tree out of partial gene trees that is annotated
by TC/IC scores, this is not supported because this would require
building some sort of supertree consensus tree that is by itself a very
difficult problem, hence we decided to not consider this.

All the best,

Alexis

>
> Thanks in advance,
> Will
>
> --
> William Gearty
> PhD Student, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences

> people.stanford.edu/wgearty <http://people.stanford.edu/wgearty>
>
> --
> 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>.
> For more options, visit https://groups.google.com/d/optout.

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[William Gearty]

Hi Alexis,

Ah, that makes much more sense, thanks for the clarification!

Everything works now (although I think you have the -z and -t commands backwards).

Thanks,

Will

To unsubscribe from this group and stop receiving emails from it, send an email to raxml+un...@googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

--

William Gearty

PhD Student, Paleobiology

Department of Geological Sciences

Stanford School of Earth, Energy & Environmental Sciences

people.stanford.edu/wgearty

[Alexandros Stamatakis]

yes of course, the species tree is passed via -t and the (partial) gene
trees via -z ...

alexis

On 09.02.2016 18:00, William Gearty wrote:
> Hi Alexis,
> Ah, that makes much more sense, thanks for the clarification!
> Everything works now (although I think you have the -z and -t commands
> backwards).
> Thanks,
> Will
>
> On Mon, Feb 8, 2016 at 12:30 AM, Alexandros Stamatakis
> <alexandros...@gmail.com

> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.

> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>

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

>
> --
> 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>.