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TreeScaper specifications

Information


Unique identifier OMICS_13114
Name TreeScaper
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Source code URL https://codeload.github.com/whuang08/TreeScaper/zip/master
Maintained Yes

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  • person_outline Wen Huang <>

Publication for TreeScaper

TreeScaper in publications

 (2)
PMCID: 5837689
PMID: 28945862
DOI: 10.1093/sysbio/syx070

[…] robinson—foulds distances were calculated among all trees. robinson—foulds distances were transformed into two dimensions using the stochastic cca algorithm for nonlinear dimension reduction in treescaper v1.09 (). coordinates were then visualized in r using hexagonal binning in the hexbin library v1.27.1 (). nuclear and mitochondrial 50% majority rule consensus trees were generated […]

PMCID: 5290614
PMID: 28153045
DOI: 10.1186/s12859-017-1479-1

[…] cannot be fully answered, except perhaps by a subjective evaluation of the projection. we employed four different methods to estimate the intrinsic dimensionality of the rf-distances using the treescaper software package []; correlation dimension [, ], a maximum likelihood estimator [], a nearest neighbor estimator [] and by examining the final value of the nldr cost function versus […]


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TreeScaper institution(s)
Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA; Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA; Department of Mathematics, Florida State University, Tallahassee, FL, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA; Department of Mathematical Engineering, ICTEAM, Université catholique de Louvain, Louvain-La-Neuve, Belgium; Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
TreeScaper funding source(s)
This work was supported by the US National Science Foundation. This paper presents research results of the Belgian Network DYSCO (Dynamical Systems, Control, and Optimization), funded by the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office.

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