topiary: python framework for doing ancestral sequence reconstruction

Installation

Documentation

Try it out on Google Colab

• Go from a few initial sequences to a full alignment
• Build a phylogenetic tree and reconstruct ancestors

Features

• Automatic. Performs sequence database construction, quality control, multiple sequence alignment, tree construction, gene/species tree reconciliation, and ancestral reconstruction with minimal user input.

• Species aware. Integrates with the Open Tree of Life database, improving selection of sequences and tree/ancestor inference.

• Human-oriented. Users prepare input as spreadsheets, not arcane text files. Outputs are spreadsheets, clean fasta files, pdf trees, and graphical summaries of ancestor quality.

• Flexible. Use as a command line program or do custom analyses and plotting with the API.

• Modern. Topiary is built around a collection of modern, actively-supported, phylogenetic software tools:

  • OpenTree
  • muscle 5
  • RAxML-NG
  • GeneRax
  • PastML
  • toytree

Citing topiary

Orlandi KN, Phillips SR, Sailer ZR, Harman JL, Harms MJ. "Topiary: pruning the manual labor from ancestral sequence reconstruction" (2022) Protein Science doi: 10.1002/pro.4551