Target audience: University students (BSc) inn Earth Sciences or Biology

Discipline: Earth sciences, geoscience, Evolutionary biology

The exercise assumes that you have a character matrix in .xlsx format. The first column are names of taxa. You can run the script in Python/Phylogenetic_tree.py to import this matrix into Python, use scikit-bio to create a tree using the neighbor-joining method and save the tree in the Newick format.

The script assumes that there is a matrix.xlsx file in the same folder as the script, so in Python. You can copy your matrix into that folder and make sure it's called matrix.xlsx or change the path in the script.

The script saves a tree file called tree.newick in the same folder. You can view this filed using many software packages for phylogenetic analyses, as well as online using ETE's TreeViewer.

Activate the virtual environment by typing the following in your terminal:

poetry install

after that you can type:

poetry run python Python/Phylogenetic_tree.py

*** TBC: add options for users not familiar with venvs ***

If you would like to contribute to this OER, please see CONTRIBUTING.md.

Please see LICENSE.md

Emilia Jarochowska
Utrecht University
email: e.b.jarochowska [at] uu.nl
Web page: www.uu.nl/staff/EBJarochowska
ORCID: 0000-0001-8937-9405

Niklas Hohmann
Utrecht University
email: n.h.hohmann [at] uu.nl
Web page: www.uu.nl/staff/NHohmann
ORCID: 0000-0003-1559-1838

Copyright 2024 Utrecht University