tree_sisters
Installation
tree_sisters can be installed by unzipping the source code in one directory and using this command:
sudo python setup.py install
You can also install it directly from the Python Package Index with this command:
sudo pip install tree_sisters
Usage
To get info on all lineages in a decorated newick tree:
tree_sisters -t a.tree >lineages.csv
This will print out, for each leaf, the leaf ID, the taxonomy containing that leaf, and lineage(s) that the leaf is sister to.
To print out a subset of leaves in a newline separated file,
tree_sisters -t a.tree -l leaves_list.txt >lineages.csv
The a.tree file should decorated e.g. witht tax2tree (t2t decorate), which in turn requires the tree to be rooted at the base of the taxonomy e.g. (t2t reroot.)
Licence
See file LICENCE.txt in this folder
Contribute
tree_sisters is an open-source software. Everyone is welcome to contribute !