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Questions tagged [etetoolkit]

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

The ETE tookit is a Python framework for working trees.

It features a OO model for trees, visualization and annotation support as well as Jupyter notebook integration.

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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?
Gab-1997
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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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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 of node as rectangle (I found circle, square and…
Liis Kolberg
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python root two trees on the same root node

I wrote a program which calculates the distance between two trees. The trees are already rooted. I want to make sure that the trees are rooted on the same root or outgroup. As far as I know, in ete2 one can only set the root but cannot find the root…
IssnKissn
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ete2 how to operate if a node is a pair of coordinates

I need to store and then operate (add new nodes, search through, etc) a tree where every node is a pair of x,y coordinates. I found ete2 module to work with trees, but I can't catch how to save a node as a tuple or list of coordinates. Is it…
Olga
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python ete2 delete node from tree

I'm trying to remove a set of nodes from a given tree file. Input : tree file+ txt file contains the name of nodes that should only exists in the tree. this is my code: ` def find_id(file,id): f= open(file) s = open(file).read() if…
AWRAM
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ETE2: adding image to nodes

I have been trying to add different images to nodes in a phylogenetic tree using the ete2 software in Python, but have no success. from ete2 import Tree, TreeStyle, NodeStyle, TextFace, faces, add_face_to_node, AttrFace ts.show_leaf_name =…
user2167759
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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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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-latest-MacOSX-x86_64.sh' -o…
P.Brian.Mackey
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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 have no idea what my next step should be.
Gab-1997
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python ete2 TreeNode check if it has attribute

I have a tree t which some of its nodes has an attribute 'a' I want to test if a given node has this attribute, what I did is if not n.a: print "no a " but I'm getting an error treenode n has no attribute a Any way to test it ?
AWRAM
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Newick Standard and Overlaying other data

I am currently working with a massive Newick Tree. I am looking for an efficient way to overlay some other data I have about the nodes. I have tried using dendroscope and ETE but have little luck as ETE cannot handle my tree as it is massive and…
user2524994
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Save path from leaves to root using ete2

I have a large tree where I want to get for each leaf node the path (all nodes) till the root. I'm trying to do this using ete2 but the tree is so large and it seems to be too slow. Can anyone suggest a faster way to do so? thats what I'm doing: …
ifreak
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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 information about this in the documentation nor on this…
globglogabgalab
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ETE2 .phonehome() Is it an Easter Egg?

ETE2 (a Python Environment for phylogenetic Tree Exploration) has a method .phonehome() which can be called on tree/node class objects. This returns: == Calling home... Got answer! He11o alien, How is everything in the Earth? We miss you in Brodo…
hello_there_andy
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