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MTR specifications

Information


Unique identifier OMICS_16676
Name MTR
Alternative name Multiple Taxonomic Ranks
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, MATLAB
Computer skills Advanced
Stability Stable
Maintained No

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Publication for Multiple Taxonomic Ranks

MTR citations

 (4)
library_books

Taxonomic Separation of Hippocampal Networks: Principal Cell Populations and Adult Neurogenesis

2016
Front Neuroanat
PMCID: 4783399
PMID: 27013984
DOI: 10.3389/fnana.2016.00022

[…] in terms of the size of its' principal cell populations, the degrees of convergence and divergence of interconnected cell populations and adult neurogenic cell populations separate species groups at multiple taxonomic ranks. The value of this information lies in the provision of data points that may be useful in the computational modeling of hippocampal function and the issues raised in the conte […]

library_books

Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli

2015
PLoS One
PMCID: 4420551
PMID: 25942314
DOI: 10.1371/journal.pone.0125495

[…] rther investigate the changes in the microbiota composition following the T. muris infection, we analysed the microbiota composition in a taxa summary plot on family level (), statistical analysis on multiple taxonomic ranks (), heat-mapping at genus level, including hierarchical cluster analysis (), and phylogenetic tree analysis to identify candidates at species level (). Hierarchical cluster an […]

library_books

Analytical Tools and Databases for Metagenomics in the Next Generation Sequencing Era

2013
PMCID: 3794082
PMID: 24124405
DOI: 10.5808/GI.2013.11.3.102

[…] t hit to the use of LCA, modified LCA, or more complicated phylogenetic inferences. Among the popularly used tools, MEGAN uses the NCBI nr database for searching and LCA algorithms for assignment []. MTR and SOrt-ITEMS modified MEGAN's LCA algorithm by use of taxonomic information shared by hits (MTR) or by performing a reciprocal BLAST hit to reduce false positive hits (SOrt-ITEMS) [, ]. MG-RAST […]

library_books

A comparative evaluation of sequence classification programs

2012
BMC Bioinformatics
PMCID: 3428669
PMID: 22574964
DOI: 10.1186/1471-2105-13-92

[…] in this paper combine all three approaches).Programs that primarily utilize sequence similarity search include CARMA [,], FACS [], jMOTU/Taxonerator [], MARTA [], MEGAN [], MetaPhyler [], MG-RAST [], MTR [], and SOrt-ITEMS []. Most of these programs employ BLAST (most commonly, BLASTX), and several incorporate some version of the lowest-common ancestor (LCA) algorithm first pioneered by MEGAN. Aft […]

Citations

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MTR institution(s)
Radboud University Nijmegen, Institute for Computing and Information Sciences, Nijmegen, The Netherlands; ICAR-CNR, Institute of High Performance Computing and Networking, Rende, Italy; Radboud University Nijmegen, IWWR, Department of Microbiology, Nijmegen, The Netherlands
MTR funding source(s)
This work was partially supported by Netherlands Organization for Scientific Research (NWO) within NWO project 600.065.120.09N213.

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