TreeClimber statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TreeClimber

Tool usage distribution map

This map represents all the scientific publications referring to TreeClimber per scientific context
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TreeClimber specifications


Unique identifier OMICS_14305
Name TreeClimber
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A file containing one or more trees and a file containing the exact name of each sequence and a simple descriptor for what treatment the sequence belongs to.
Output data Generates a file whose root is the same as the tree file name and has the extension “*.p”.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes




No version available



  • person_outline Jo Handelsman

Publication for TreeClimber

TreeClimber citations


Metagenomics: Tools and Insights for Analyzing Next Generation Sequencing Data Derived from Biodiversity Studies

Bioinform Biol Insights
PMCID: 4426941
PMID: 25983555
DOI: 10.4137/BBI.S12462

[…] he programming language PYTHON.Another widely used software for the analysis of microbial communities is Mothur. It was created from the combination of pre-existing software, such as DOTUR, SONS, and Treeclimber, but, due to the community support it has received, currently it incorporates many more algorithms, thus providing the user with a variety of choices.More recently, a web-based application […]


Comparison of next generation sequencing samples using compression based distances and its application to phylogenetic reconstruction

BMC Res Notes
PMCID: 4057587
PMID: 24886411
DOI: 10.1186/1756-0500-7-320

[…] o assess the clustering and classification ability of the alignment-free distances, we used the parsimony score to measure how different a clustering tree is from the true classification (using tools TreeClimber[], mothur[]). The parsimony score of a clustering tree is calculated by the tool TreeClimber as follows. First, the parsimony score is set to 0 and the leaf nodes are labeled according to […]


Comparison of metagenomic samples using sequence signatures

BMC Genomics
PMCID: 3549735
PMID: 23268604
DOI: 10.1186/1471-2164-13-730

[…] based on pair-wise dissimilarity matrix of multiple samples, using average-linkage for measuring the dissimilarity of two clusters. We used the phangorn[] package in R for this algorithm. We used the TreeClimber package [], a tool to compare clustering of microbial communities, to evaluate the resulting clustering trees by the parsimony test. The parsimony score measures how far away the clusterin […]

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TreeClimber institution(s)
Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
TreeClimber funding source(s)
This work was supported by a USDA postdoctoral fellowship in soil biology (2003-35107-13856), by the NSF Microbial Observatories program (MCB-0132085), by the Howard Hughes Medical Institute, and by the University of Wisconsin—Madison College of Agricultural and Life Sciences.

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