Welcome to Capybara’s documentation!

Capybara is a desktop GUI application for solving the Phylogenetic tree reconciliation problem.

Its key features are also available as a Python package.

Keywords: Cophylogeny reconstruction, phylogenetic tree reconciliationm, enumeration.

Overview

Phylogenetic tree reconciliation is the method of choice in analyzing host-symbiont systems. Despite the many reconciliation tools that have been proposed in the literature, two main issues remain unresolved:

  • listing suboptimal solutions (i.e., whose score is “close” to the optimal ones), and
  • listing only solutions that are biologically different “enough”.

The first issue arises because the optimal solutions are not always the ones biologically most significant; providing many suboptimal solutions as alternatives for the optimal ones is thus very useful. The second one is related to the difficulty to analyze an often huge number of optimal solutions.

Capybara addresses both of these problems in an efficient way. Furthermore, it includes a tool for visualizing the solutions that significantly helps the user in the process of analyzing the results.

Features

Capybara has some features in common with its predecessor EUCALPYT [1]: counting the number of optimal reconciliations, listing optimal reconciliations to a file, keeping only the acyclic ones (the definition of cyclicity is taken from [2]).

Capybara also has some exciting new features:

The counting and enumeration features of Capybara’s Optimal enumeration are also avaible as a Python package.

References

[1]Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi, and Marie-France Sagot. Eucalypt: efficient tree reconciliation enumerator. Algorithms for Molecular Biology, 10(1):3, 2015. doi: 10.1186/s13015-014-0031-3.
[2]Maureen Stolzer, Han Lai, Minli Xu, Deepa Sathaye, Benjamin Vernot, and Dannie Durand. Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics, 28(18):i409–i415, 2012. doi: 10.1093/bioinformatics/bts386.