Topiary examples

This repository contains Jupyter notebooks demonstrating the topiary ancestral sequence reconstruction package. To download all demonstration notebooks and data you can clone this repository with git or select Code -> Download ZIP above.

Demonstration notebooks

Click the colab link to run the notebook in google colab. Alternatively, you can download the notebooks and run them on a local computer. Running the notebooks requires you to install topiary.

Seed to alignment

Notebook walks through how to make a seed dataset for use in a topiary analysis, then demonstrates the seed_to_alignment pipeline that takes a seed dataset with a handful of sequences and generates a large multiple sequence alignment.

Alignment to ancestors

Notebook shows how to go from a topiary alignment to ancestral sequences. It demonstrates the alignment_to_ancestors pipeline, which identifies the maximum likelihood phylogenetic model, generates a maximum likelihood gene tree, reconciles the gene and species trees (if appropriate), and generates ancestral sequences. It also demonstrates the bootstrap_reconcile function, which generates bootstrap supports on the reconciled gene/species tree.

API example: Seed to alignment

Notebook Demonstrates the steps of the seed_to_alignment pipeline as individual API calls.