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Updated: Oct 11, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set.

David Schaller¹, Marc Hellmuth², Peter F Stadler^3,4,5,6,7,8

¹Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.

Algorithms for Molecular Biology : AMB

|December 7, 2021

Summary

A new algorithm, LinCR, efficiently constructs common refinements for rooted trees with shared leaf sets. This mathematical phylogenetics tool is simpler and faster than existing methods.

Keywords:

Compatibility of rooted trees Mathematical phylogenetics Rooted trees

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Last Updated: Oct 11, 2025

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Area of Science:

Mathematical Phylogenetics
Computational Biology
Tree Theory

Background:

The supertree problem involves finding a common refinement of rooted trees, a key challenge in mathematical phylogenetics.
While solvable in linear time for common leaf sets, existing methods are complex and inefficient.
Current approaches refine trees individually and then check for isomorphism, which can be computationally intensive.

Purpose of the Study:

To introduce LinCR, a novel algorithm for constructing the common refinement of multiple rooted trees.
To provide an efficient and simpler alternative to existing methods for solving the supertree problem.

Main Methods:

Developed an O(k|L|) algorithm named LinCR.
Employs a bottom-up approach to explicitly compute the parent function of the common refinement tree (T).
Focuses on the special case where k input trees share a common leaf set L.

Main Results:

LinCR successfully constructs the common refinement T of k input trees with a common leaf set L.
The algorithm achieves a time complexity of O(k|L|).
Demonstrated superior performance compared to existing asymptotically optimal algorithms in empirical tests.

Conclusions:

LinCR offers a simpler implementation compared to other optimal algorithms for the supertree problem.
Empirical comparisons show LinCR outperforms alternative methods.
An open-source Python implementation of LinCR is available for use in phylogenetic analyses.