tqDist: a library for computing the quartet and triplet distances between binary or general trees
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 for the triplet distance calculation and for the quartet distance calculation, where n is the number of leaves in...
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| Published in | Bioinformatics (Oxford, England) Vol. 30; no. 14; pp. 2079 - 2080 |
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| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
15.07.2014
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1367-4811 |
| DOI | 10.1093/bioinformatics/btu157 |
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| 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 for the triplet distance calculation and 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 .
Contact: cstorm@birc.au.dk
Supplementary information: Supplementary data are available at Bioinformatics online |
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| AbstractList | 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 for the triplet distance calculation and 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 .
Contact: cstorm@birc.au.dk
Supplementary information: Supplementary data are available at Bioinformatics online 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.UNLABELLEDtqDist 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.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.AVAILABILITY AND IMPLEMENTATIONtqDist 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. 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. 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. |
| Author | Johansen, Jens Pedersen, Christian N. S. Brodal, Gerth Stølting Mailund, Thomas Sand, Andreas Holt, Morten K. |
| Author_xml | – sequence: 1 givenname: Andreas surname: Sand fullname: Sand, Andreas – sequence: 2 givenname: Morten K. surname: Holt fullname: Holt, Morten K. – sequence: 3 givenname: Jens surname: Johansen fullname: Johansen, Jens – sequence: 4 givenname: Gerth Stølting surname: Brodal fullname: Brodal, Gerth Stølting – sequence: 5 givenname: Thomas surname: Mailund fullname: Mailund, Thomas – sequence: 6 givenname: Christian N. S. surname: Pedersen fullname: Pedersen, Christian N. S. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24651968$$D View this record in MEDLINE/PubMed |
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| References_xml | – volume: 7 start-page: e35025 year: 2012 ident: 2023012711242127400_btu157-B11 article-title: Cultural phylogenetics of the Tupi language family in Lowland South America publication-title: PLoS One doi: 10.1371/journal.pone.0035025 – volume: 45 start-page: 323 year: 1996 ident: 2023012711242127400_btu157-B4 article-title: The triples distance for rooted bifurcating phylogenetic trees publication-title: Syst. Biol. doi: 10.1093/sysbio/45.3.323 – volume: 323 start-page: 479 year: 2009 ident: 2023012711242127400_btu157-B6 article-title: Language phylogenies reveal expansion pulses and pauses in pacific settlement publication-title: Science doi: 10.1126/science.1166858 – volume: 34 start-page: 193 year: 1985 ident: 2023012711242127400_btu157-B5 article-title: Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units publication-title: Syst. Biol. doi: 10.2307/sysbio/34.2.193 – volume: 6 start-page: 15 year: 2011 ident: 2023012711242127400_btu157-B9 article-title: A sub-cubic time algorithm for computing the quartet distance between two general trees publication-title: Algorithms Mol. Biol. doi: 10.1186/1748-7188-6-15 – volume-title: Proceedings of 16th Workshop on Algorithm Engineering and Experiments (ALENEX) Portland, Oregon, USA. year: 2014 ident: 2023012711242127400_btu157-B7 article-title: On the scalability of computing triplet and quartet distances doi: 10.1137/1.9781611973198.2 – volume-title: Phylogenetics year: 2003 ident: 2023012711242127400_btu157-B10 doi: 10.1093/oso/9780198509424.001.0001 – volume-title: Mathematics in the Archaeological and Historical Sciences year: 1971 ident: 2023012711242127400_btu157-B3 article-title: The recovery of trees from measures of dissimilarity – start-page: 1814 volume-title: ACM-SIAM Symposium on Discrete Algorithms (SODA)New Orleans, Louisiana, USA year: 2013 ident: 2023012711242127400_btu157-B2 article-title: Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree – volume: 38 start-page: 377 year: 2004 ident: 2023012711242127400_btu157-B1 article-title: Computing the quartet distance between evolutionary trees in time O(n log n) publication-title: Algorithmica doi: 10.1007/s00453-003-1065-y – volume: 20 start-page: 1636 year: 2004 ident: 2023012711242127400_btu157-B8 article-title: QDist–quartet distance between evolutionary trees publication-title: Bioinformatics doi: 10.1093/bioinformatics/bth097 |
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| Title | tqDist: a library for computing the quartet and triplet distances between binary or general trees |
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