Andreas Sand1, Morten K Holt2, Jens Johansen2, Gerth Stølting Brodal1, Thomas Mailund2, Christian N S Pedersen1. 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.
Abstract
UNLABELLED: 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.
UNLABELLED: 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.
Authors: Daniel Novikov; Sergey Knyazev; Mark Grinshpon; Pelin Icer; Pavel Skums; Alex Zelikovsky Journal: J Comput Biol Date: 2021-10-25 Impact factor: 1.479
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