All Questions
Tagged with etetoolkit or ete4
29 questions
0
votes
1
answer
238
views
How to display multiple trees simultaneously with ete3?
I debuted recently on ete3 (on Python3), and for debugging purposes I would find convenient to display two trees side to side, as in matplotlib.pyplot.subfig for instance. However, I found no ...
- 616
1
vote
1
answer
1k
views
Error installing etetoolkit. When installing using anaconda
I followed the directions to install etetoolkit for mac.
# Install Minconda (you can ignore this step if you already have Anaconda/Miniconda)
curl -L 'http://repo.continuum.io/miniconda/Miniconda3-...
- 44.5k
1
vote
0
answers
237
views
How to pass a Dendropy object with metadata to ete3 in python3?
If I have a dendropy tree that I annotate with some metadata, for example with some taxonomies, how can I convert the whole tree with metadata into a ete3 object?
import dendropy
t = dendropy.Tree....
- 397
1
vote
1
answer
6k
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ete3 module on python3 - cannot import TreeStyle, faces, AttrFace, NodeStyle
I a linux user and so far I've using ete3 in python2 succesfully.
I installed ete3 for python3 and there are certain modules that python3 can't find. I believe I have all the dependencies installed ...
- 397
2
votes
1
answer
3k
views
How can I get taxonomic rank names from taxid?
This question is related to:
How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?
The solution given there works but I would like to have the ...
- 61
1
vote
1
answer
220
views
Different guiding_lines_colos for different leaf nodes in ETE3 using TreeStyle class or anything else
How how can I add different colors for guiding line (connecting leaf node with the text using guiding_lines_color in TreeStyle class) in ETE3 python module.
Thanks
- 335
3
votes
1
answer
3k
views
How to color leaves on `ete3` Tree? (Python 3)
I just started using ete3 and it is awesome.
How can I color the leaves of an ete3 Tree object using a color dictionary? I made "c":None because I don't want the of c to show up.
I want to have ...
- 31.1k
1
vote
1
answer
184
views
How to convert a tree drawn with ete2 to Newick format?
I have drawn a tree in python using ete2 commands Tree(), .add_child(), .add_sister() and so on.
Is there any way I can convert this tree to the corresponding Newick format?
- 31
0
votes
1
answer
1k
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How to install ete2 on Python 2.7?
I have looked at some other questions about module installation and Python documentation, but I cannot succeed in installing ete2 on Python 2.7.
I have already downloaded it from the website, but ...
- 31
8
votes
3
answers
5k
views
How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?
I have a list of taxids that looks like this:
1204725
2162
1300163
420247
I am looking to get a file with taxonomic ids in order from the taxids above:
kingdom_id phylum_id class_id ...
- 397
4
votes
1
answer
986
views
How to change the font orientation on node labels with ETE Toolkit (Python)
I'd like to change the orientation of font faces on the output image that is produced by ETE Toolkit: http://etetoolkit.org
For some reason rotation and orientation change does not affect to labels ...
- 990
1
vote
0
answers
1k
views
error using ete3 in python: 'No module name cPickle'
I'm having a problem similar to:
Theano import error: No module named cPickle
But with using ete3 (www.etetoolkit.org). I downgraded to ete2 and the problem disappeared, but would like to be using ...
- 1,305
2
votes
1
answer
339
views
How can I create a tree using the python package ete2 using strings stored in a list?
I am trying to make a phylogenetic tree using the python package ete2 from synthetic data output from a cellular automaton model of mine. The data consists of pairs listed as (parent, child) where ...
- 1,305
1
vote
1
answer
280
views
Rectangle as NodeStyle shape in ete2
I would like to create my own layout for dendrogram in ete2. I have very specific needs to customize the tree node by node (i.e every node has different style etc..)
Is it possible to set the shape ...
- 163
3
votes
1
answer
2k
views
ETE2 - One Child Node with Multiple Parents?
I'm trying to create a tree using the ETE2 module in Python. I'd like to add 1 child node to 2 parent nodes so that they both connect to the child when the tree is displayed. I'm a complete novice ...
- 283
