RAxML-EPA output files

[Frédéric Delsuc]

Hi,

Could someone please tell me what exactly are the values reported in the last two columns of the "RAxML_classification" file resulting from an RAxML-EPA analysis?

Example:

ZOO-064b_M13F I29 1 0.00178454802854413749

ZOO-065a_M13-F I29 1 0.00168648656206445645

ZOO-066a_M13-F I29 1 0.00712137782479591291

13297Y14_M13-R I139 1 0.00000100000050002909

Thanks!

Fred   

[Alexandros Stamatakis]

Dear Fred,

The third column is just the number of times that read was inserted into
that branch (this should be always one, it's a left-over from the
bootstrapping procedure that was later removed again),.

The 4th column is the so-called pendant branch length, that is, the
branch length leading to the placed read/query sequence.

I would recommend that you rather use the standardized .jplace output
format that is also generated by RAxML-EPA:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009

it can be visualized with:

http://itol3.embl.de/

and post-analyzed with:

http://genesis-lib.org/

alexis

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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

[Frédéric Delsuc]

Hi Alexis,

Thanks for your answer.

We are also using the standardized jplace file and its display in iTol and post analysis by Genesis but I was kind of puzzled by the fact that in this particular file the 3rd column was always 1.

Best wishes,

Fred

[Alexandros Stamatakis]

:-)

alexis

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> Alexandros (Alexis) Stamatakis
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> 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>

[lucas...@h-its.org]

Hi Frédéric,

thanks for using Genesis! Let me know if you have any questions.
What kind of post-analysis are you doing, and is there any feature missing in Genesis that you'd need? I'm always looking for inspiration ;-)

Lucas

[Frédéric Delsuc]

Hi Lucas,

So far we are using the Genesis library to display jplace trees summarizing evolutionary placements on a reference tree with colored branches.

And it's working well :) Thanks!

What would be great would be to produce an iTOL-like visualization with circles, but I guess that you are dependent on FigTree that does not allow such a display.

Fred  

[lucas...@h-its.org]

Hi Fred,

sorry for the late answer. For the visualisation with coloured branches, I used FigTree simply because it was easy to write out files in their format. It is however not a big issue to add more output file formats.

I looked at the annotation capabilities of FigTree - it only supports shapes at nodes, not at edges (see attachment). Same for Dendroscope. So, if you want to summarize the placement mass per branch as the size of a circle (for example), this works: As the reference tree can be drawn rooted, you can interpret the shape at the node as belonging to the edge towards the root. For your own visual inspection, this should suffice, but for a publication figure, you'd probably want the shape to sit at the branch instead.

Also, if you don't want to summarize the data, but instead visualize each placement position as a shape, this does not work. So, if you know of a tree viewer that supports adding shapes along the branches, let me know. It should be possible to write some file format for such a viewer.

Lucas