FigTree/Dendroscope cannot read a newick tree generated dy SUMTREES

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Alexei Kassian

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Mar 28, 2019, 12:48:13 PM3/28/19
to DendroPy Users
Hi all,
I have a newick tree produced by SUMTREES - result.tre (attached).
FigTree cannot read it and returns the following error: Number format error: For input string: "0.00833...
Dendroscope also fails.
What should I change in this txt file to make it readable?
result.tre

Jeet Sukumaran

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Mar 28, 2019, 12:57:00 PM3/28/19
to dendrop...@googlegroups.com, Alexei Kassian
The NEWICK string has metadata annotations. Neither FigTree nor
Dendroscope understand this in NEWICK format, but they do in NEXUS format.

Solution:

(1) convert your file to NEXUS

or

(2) remove the metadata annotations (the stuff in square brackets)

FYI, if you upgrade to the latest development version of DendroPy you
can take advantage of the new ``dendropy-format.py`` utility to make the
conversion:

~~~
dendropy-format \
--from newick \
--to nexus \
result.tre > result.nex
~~~


You can upgrade by, for e.g.,:

~~~
python -m pip install --upgrade
git+https://github.com/jeetsukumaran/DendroPy.git@development-master
~~~


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Alexei Kassian

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Mar 28, 2019, 3:18:45 PM3/28/19
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Dear Jeet,
thank you, it works. Just to add: the third option (probably the easiest one) is to generate NEXUS directly by SUMTREES via the flag '-F nexus'.
Best,
Alexei

четверг, 28 марта 2019 г., 19:57:00 UTC+3 пользователь Jeet Sukumaran написал:
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