QDist specifications

Information


Unique identifier OMICS_15537
Name QDist
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The trees in Newick format
Output data The quartet distance between the trees, the summary statistics
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Christian Pedersen <>

Publications for QDist

QDist in publications

 (7)
PMCID: 5429014
PMID: 27436281
DOI: 10.1093/jxb/erw256

[…] only the third position of codons. the gtr+gamma+i mutation model was used in both analyses. resulting trees were then compared with the species phylogeny and tested for topological congruence using qdist (). failing both phylogenetic congruence tests resulted in exclusion from further analysis. finally 6784 ortholog groups were obtained., the branch model of paml 4.2 () was used to calculate […]

PMCID: 3958223
PMID: 24556671
DOI: 10.3390/s140203342

[…] on the distribution quality should be judged in terms of visual homing. the chosen measure of quantitative characterization of distribution, similar to the one proposed in [], is defined as: (17)qdist=1o×s∑o=1o∑s=1s(−∑i=1nospilog2pi)where pi is the ratio of matching features in the ith sector ring over all the ones in the scale layer (s) of the octave (o). if the correctly matching features […]

PMCID: 3762195
PMID: 23843191
DOI: 10.1093/gbe/evt105

[…] similarity (), we also calculated topological distances between trees. the topological distances between trees were calculated using the normalized quartet distance, as implemented in the program “qdist” () version 2.0, downloaded from http://birc.au.dk/software/qdist/., note that an increase in congruence between tree topologies results in an increase in the cpcc and a decrease in the quartet […]

PMCID: 3323632
PMID: 22506065
DOI: 10.1371/journal.pone.0035025

[…] of expert trees and asjp trees for the tupi-guarani subgroup, obtaining normalized split distances using splitdist (http://birc.au.dk/software/splitdist/) and normalized quartet distances using qdist (http://birc.au.dk/software/qdist). for the split distances we use an asymmetric distance measure that counts the number of splits in the first tree that are not found in the second, […]

PMCID: 3141660
PMID: 21639882
DOI: 10.1186/1748-7188-6-15

[…] can have a running time significantly better than the theoretical upper bound, depending on the topology of the trees being compared., the software is available from http://www.birc.au.dk/software/qdist. it has been tested on ubuntu linux and mac os x., the authors declare that they have no competing interests., jn, tm and cp developed the algorithm. ak implemented the algorithm. ak and jn […]


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QDist institution(s)
Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark

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