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Questions tagged [ete3]

Use for questions related to the ETE toolkit version 3, a Python framework to work with trees.

36 questions
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How can overlapping nodefaces be generated in ETE3?

I want to generate overlapping node faces. Currently, vertical distance (y-coordinate) of nodes changes with the size of node face. If you know how to achieve overlapping node face, please share the code. Thanks
Manu
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'Module' has no attritube 'Treestyle'

If found some hits on stackoverflow where people have issues using ete3 tools when PyQT4 is not installed, and this (used to) also apply for me. However, I've now tried to reinstall a piece of software and it keeps complaining about 'Module' has no…
user2810298
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How to correctly update an empty ete3.Tree object with a newick formatted tree string [Python]?

I'm creating a class that inherits from ete3.Tree. I want to add a newick formatted string to the object but I can't figure out the correct way to update the object. I want t2 below to be the same structure as t1 and by structure I mean to be the…
O.rka
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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.get_from_string("(A,(B,(C,D)));",…
aLbAc
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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 according to the instructions. I can import ete3,…
aLbAc
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Rendering tree with ete3 package messes up menus in tkinter

I'm designing a desktop application using tkinter for the GUI. The application generates some nested data structures that I want to render graphically as trees. For that, I'm using the ete3 package. However, when I render the trees into an image…
Cartucho
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Python ete3 - Is there a way to stretch branches of phylogenetic trees?

I am trying to read a phylogenetic tree and stretch its branches to be bigger or smaller than the original, but I didn't find how. The stretch needs to be on the tree itself - not on its visualization. For example, the following code reads a tree…
Yair
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python ete3 - failure to create pdf after Gtk warning

I have run into a problem that I do not find any helpful information on. I am using ete3 in python to automatize the creation of phylogenetic tree figures. I have written some code that works wonderful if I execute it in my ipython…
sequence_hard
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Loading NCBITaxa crashes

I've been using the ete2 module on very powerful servers for some time. Everything was fine until it started going very slowly (one get_taxid_translator() function per minute), now I cannot even get past ncbi = NCBITaxa() assignment. I have…
Alexis Lucattini
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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
Manu
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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 the functionality in ete3. Following after the…
cancerconnector
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Ete3 build - ValueError: Error parsing Phyml result

Hello, I am using ete3 build to build a phylogeny of my target species. I ran the following command: ete3 build -a eteinput.faa --cogs outfile.tab -o test1_results -m sptree_fasttree_85 -w full_modeltest_bootstrap --clearall --cpu 20 I am…
Nitin Ravikanthachari
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What can I use in Python to create a visualization of a flowchart with data shown inside the nodes as boxes?

I am looking for a way to create a graph/flowchart in Python that will allow me to create nodes as boxes of multiple values of data (ideally separated into different lines of information such as shown in one of the boxes in the picture). So far, I…
Spiinner
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"clean" ete3 tree from super short branches

my tree building tool likes binary trees. in order to get such trees it often introduces super small branches to keep it in a binary structure. this is super annoying for me when i try to compare trees since those small branches introduce splits…
tristan
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ete3 error : could not be translated into taxids! - Bioinformatics

I am using ete3(http://etetoolkit.org/) package in Python within a bioinformatics pipeline I wrote myself. While running this script, I get the following error. I have used this script a lot for other datasets which don't have any issues and have…
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