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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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Documentation


Maintainer


  • person_outline Jo Handelsman

Publication for TreeClimber

TreeClimber citations

 (3)
library_books

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

2015
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 […]

library_books

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

2014
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 […]

library_books

Comparison of metagenomic samples using sequence signatures

2012
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 […]

Citations

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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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