Welcome to Espalier’s documentation!

Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests. The package can be used to compute maximum agreement forests, compute subtree-prune-and-regraft (SPR) distances, reconcile discordant trees and reconstruct ancestral recombination graphs (ARGs).

Contents:

• Introduction
  • Motivation
  • Installation/Usage
  • Requirements
• Espalier Primer
  • Installation
  • Computing Maximum Agreement Forests
  • Computing SPR distances
  • Tree reconciliation through MAFs
  • Reconstructing Ancestral Recombination Graphs
  • Automated breakpoint detection
• Command Line Interface
  • Usage
  • Computing Maximum Agreement Forests
  • Computing SPR distances
  • Tree reconciliation
  • ARG reconstruction

Indices and tables

• Index

• Module Index

• Search Page