Cannot read custom threshold consensus with FigTree

[Frank Stokvis]

Hi all,

I'm trying to create a 60% cut-off consensus tree with RAxML form a previous run using:

raxmlHPC -J T_60 -z RAxML_bootstrap.Bootstraps -m GTRCAT -n 60 > STDOUT.consensus.log

The file created gives the following FigTree error:

Number format error: For input string: "1.0[62]"

My questions:
- Am I doing this correctly?
- Which of the previous run files do I exactly need?
- Is the following solution the only one?

https://groups.google.com/forum/#!topic/raxml/Gij0QBZmszA

the consensus trees produced by RAxML follow the format 
":length[support]", which is not supported in figtree (and maybe also 
in treeedit?). Dendroscope and Treeview should be able to open these 
files, though. If you prefer figtree (like I do), you can use a work 
around: 
open the consensus treefile in a text editor that is able to handle 
regular expressions (I use on mac "textwrangler" and on pc "notepad+ 
+") and open the replace function and exchange every 

([:]\d+[.]\d+)[[](\d+)[]] 

for 

\2\1 

afterwards figtree is able to read your file.

Cheers,

Frank

[Alexandros Stamatakis]

> I'm trying to create a 60% cut-off consensus tree with RAxML form a
> previous run

> <https://drive.google.com/drive/folders/0B9VULIBkJsrEYU1GS3NJQWhpZms?usp=sharing>

> using:
>
> raxmlHPC -J T_60 -z RAxML_bootstrap.Bootstraps -m GTRCAT -n 60 >
> STDOUT.consensus.log
>
> The file created gives the following FigTree error:
>
> Number format error: For input string: "1.0[62]"
>
> My questions:
> - Am I doing this correctly?

yes ...

> - Which of the previous run files do I exactly need?

you mean of RAxML? the call is correct.

> - Is the following solution the only one?

yes, I am afraid,

alexis

>
> /https://groups.google.com/forum/#!topic/raxml/Gij0QBZmszA
> <https://groups.google.com/forum/#%21topic/raxml/Gij0QBZmszA>/
> /
> /
> /the consensus trees produced by RAxML follow the format

> ":length[support]", which is not supported in figtree (and maybe also
> in treeedit?). Dendroscope and Treeview should be able to open these
> files, though. If you prefer figtree (like I do), you can use a work
> around:
> open the consensus treefile in a text editor that is able to handle
> regular expressions (I use on mac "textwrangler" and on pc "notepad+
> +") and open the replace function and exchange every
>
> ([:]\d+[.]\d+)[[](\d+)[]]
>
> for
>
> \2\1
>

> afterwards figtree is able to read your file. /
>
> Cheers,
>
> Frank
>
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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

[Frank Stokvis]

Dear Alexis,

Thank you for you quick reply!

Cheers,

Frank Stokvis

Senior research technician

071-5271912
Sylviusweg 72, 2333 BE Leiden, room 6.4.17, ma, di, do, vr
frank....@naturalis.nl, www.science.naturalis.nl

an email to raxml+unsubscribe@googlegroups.com
<mailto:raxml+unsubscribe@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

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