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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 in publications

 (11)
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 […]

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 […]

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 […]

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, […]

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 […]

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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