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TreeCmp specifications

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Unique identifier OMICS_14019
Name TreeCmp
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability No
Maintained No

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Publication for TreeCmp

TreeCmp citations

 (11)
library_books

Evolutionary Genetics of Cytoplasmic Incompatibility Genes cifA and cifB in Prophage WO of Wolbachia

2018
Genome Biol Evol
PMCID: 5793819
PMID: 29351633
DOI: 10.1093/gbe/evy012

[…] quantifying congruence scores between the cifa and cifb trees was carried out with matching cluster (mc) and robinson–foulds (rf) metrics using a custom python script previously described () and the treecmp program (). mc weights topological congruency of trees, similar to the widely used rf metric. however, mc takes into account sections of subtree congruence and therefore is a more refined […]

library_books

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar

2017
Front Microbiol
PMCID: 5563069
PMID: 28861051
DOI: 10.3389/fmicb.2017.01530

[…] congruency analysis was used to further explore the possible existence of phylosymbiosis. for this, we quantified congruence between the host phylogenetic tree and microbial dendrograms using the treecmp program. microbial dendrograms were created in qiime using both weighted unifrac and bray-curtis distances derived from otu tables averaged by frog species. using treecmp, we calculated […]

library_books

Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny

2017
Sci Rep
PMCID: 5495804
PMID: 28674428
DOI: 10.1038/s41598-017-04707-4

[…] the trees are significantly different from one another., furthermore, differences among phylogenetic trees obtained from genome, snp and mlst gene fragments data were evaluated with the software treecmp. in this analysis, two topology metrics, matching clusters and r-f clusters, were utilized. a distance value of 0 indicates that the two trees under evaluation are identical and the value […]

library_books

Using nearly full genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic

2016
Sci Rep
PMCID: 5180198
PMID: 28008945
DOI: 10.1038/srep39489

[…] of splits or clades induced by one of the trees but not the other. here, we use an approximation to the rf metric implemented in the comparetree program (http://meta.microbesonline.org/fasttree/treecmp.html), which also calculates the fraction of splits in the query tree (i.e., the reconstructed trees) that are shared with the reference one (i.e., the true trees). unlike the rf metric, […]

library_books

Alignment free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains

2016
Sci Rep
PMCID: 5120338
PMID: 27876823
DOI: 10.1038/srep37243

[…] triplets; that is, on three-element subsets of the set of species. triplet based distances provide a robust and fine-grained measure of the similarities between trees, which was developed as toolbox treecmp., the above three metrics have different characteristics and application scopes of their own. in , we constructed example trees and measure their distances with the three metrics. shows […]

library_books

Genome based microbial ecology of anammox granules in a full scale wastewater treatment system

2016
Nat Commun
PMCID: 4821891
PMID: 27029554
DOI: 10.1038/ncomms11172

[…] and a phylogenetic tree was constructed using fasttree2 (ref. ) and bootstrapped using seqboot from the phylip package and the script comparetobootstrap.pl (http://meta.microbesonline.org/fasttree/treecmp.html)., assembled 16s sequences were used for blast searches against the ncbi-nt database (december 2014), to assess the previous detection of the identified organisms (at >97% 16s rrna […]


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TreeCmp institution(s)
Department of Algorithms and Systems Modelling, Faculty of Electronics, Telecommunication and Informatics, Gdansk University of Technology, Gdańsk, Poland; Systems Modelling Laboratory, Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland; Evolutionary Systems Laboratory, Adam Mickiewicz University, Poznan, Poland
TreeCmp funding source(s)
This work was supported by the Polish Ministry of Science and Education (grant n°N303 291234) and the Polish National Science Centre (grant n°DEC-2011/02/A/ST6/00201).

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