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etetoolkit
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCB...
``` ==================================================================================== test session starts ===================================================================================== platform freebsd13 -- Python 3.9.13, pytest-7.1.2, pluggy-1.0.0 -- /usr/local/bin/python3.9 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2/.hypothesis/examples') rootdir: /disk-samsung/freebsd-ports/biology/py-ete3/work-py39/ete3-3.1.2 plugins: hypothesis-6.53.0, typeguard-2.13.3, forked-1.4.0, xdist-2.5.0 collected...
Hi, Are there plans to port `ete_toolchain` for ARM / Apple Silicon? I note that the package has not been updated for 4 years. If there are no plans, what...
Dear @jhcepas, I want to list the terminal and non-terminal nodes for the NCBITaxa tree. Since the tree is an independent object and not part of the PhyloTree class, there...
Greetings, When applying a circular layout, the leaf names are by default inverted for readability at 90 and 270 angles (attaching the example from the tutorial below, where the whole...
The `export()` function of `Phyloxml` class uses `write(..)` inconsistently. In some places, byte arguments are given to `write(..)` (e.g. Line 1681 of `ete/phyloxml/_phyloxml.py`) ```python3 outfile.write(str(self.valueOf_).encode(ExternalEncoding)) ``` whereas in other places,...
Jplace files are the outputs of phylogenetic placement papers. It is use in many software, such as RaxML, iTol ... etc ... Its newick representation introduces a supplementary field in...
I'm rendering a tree in ete3 (v3.1.2): ```python from ete3 import Tree import os os.environ['QT_QPA_PLATFORM']='offscreen' test_tree = Tree('test_file.nw') test_tree.render('tree.png') ``` And getting an error: ```python File ~/miniconda3/envs/periodic_phyla/lib/python3.10/site-packages/ete3-3.1.2-py3.7.egg/ete3/treeview/main.py:752, in save(scene, imgName,...
I am trying to run ete3 to build a species tree. Many of the COGs that I'm using have multiple sequences from the same species. I hope that this is...
Dear ete3 team, Thanks for your such amazing work. My issue is that, Suppose I have a newick file A, and a list of old and new names mapping table...
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Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCB...