TreeClimber specifications

Information


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.
Input format PHYLIP, PAUP*, MRBAYES, MEGA, NEXUS
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

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Maintainer


  • person_outline Jo Handelsman <>

Publication for TreeClimber

TreeClimber in publications

 (2)
PMCID: 4057587
PMID: 24886411
DOI: 10.1186/1756-0500-7-320

[…] 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 […]

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

[…] 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 […]


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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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