tqDist: a library for computing the quartet and triplet distances between binary or general trees

Andreas Sand; Morten K Holt; Jens Johansen; Gerth Stølting Brodal; Thomas Mailund; Christian N S Pedersen

doi:10.1093/bioinformatics/btu157

tqDist: a library for computing the quartet and triplet distances between binary or general trees

Bioinformatics. 2014 Jul 15;30(14):2079-80. doi: 10.1093/bioinformatics/btu157. Epub 2014 Mar 20.

Authors

Andreas Sand¹, Morten K Holt², Jens Johansen², Gerth Stølting Brodal¹, Thomas Mailund², Christian N S Pedersen¹

Affiliations

¹ Bioinformatics Research Centre, Department of Computer Science and MADALGO, Center for Massive Data Algorithms, a Center of the Danish National Research Foundation, Aarhus University, DK-8000 Aarhus C, DenmarkBioinformatics Research Centre, Department of Computer Science and MADALGO, Center for Massive Data Algorithms, a Center of the Danish National Research Foundation, Aarhus University, DK-8000 Aarhus C, Denmark.
² Bioinformatics Research Centre, Department of Computer Science and MADALGO, Center for Massive Data Algorithms, a Center of the Danish National Research Foundation, Aarhus University, DK-8000 Aarhus C, Denmark.

PMID: 24651968
DOI: 10.1093/bioinformatics/btu157

Abstract

tqDist is a software package for computing the triplet and quartet distances between general rooted or unrooted trees, respectively. The program is based on algorithms with running time [Formula: see text] for the triplet distance calculation and [Formula: see text] for the quartet distance calculation, where n is the number of leaves in the trees and d is the degree of the tree with minimum degree. These are currently the fastest algorithms both in theory and in practice.

Availability and implementation: tqDist can be installed on Windows, Linux and Mac OS X. Doing this will install a set of command-line tools together with a Python module and an R package for scripting in Python or R. The software package is freely available under the GNU LGPL licence at http://birc.au.dk/software/tqDist.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Classification / methods
Phylogeny*
Software*