:: DESCRIPTION
IM-TORNADO is a pipeline for analysis of paired-end 16S rDNA amplicon data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries.
Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher JP, Chia N.
PLoS One. 2014 Dec 15;9(12):e114804. doi: 10.1371/journal.pone.0114804. eCollection 2014.
:: DESCRIPTION
TreeMaker is a software that allows the interactive building and editing of a taxonomy and its conversion into a phylogeny for the above calculations. It also allows the editing of site abundance and species richness data. This data may be imported from and exported to a variety of formats for interoperability with other programs. While it is mainly intended for use in conservation and biodiversity, it can be used as a simple tool for building phylogenies.
::DEVELOPER
Paul-Michael Agapow, Dept. Biology, University College London
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ross H Crozier, Lisa J Dunnett, Paul-Michael Agapow (2005).
Phylogenetic biodiversity assessment based on systematic nomenclature.
Evolutionary Bioinformatics Online 1:11-36.
:: DESCRIPTION
The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment
::DEVELOPER
The Ribosomal Database Project
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR.
Appl Environ Microbiol. 2007 Aug;73(16):5261-7. Epub 2007 Jun 22.
:: DESCRIPTION
HTTMM is a package designed for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1112-22. doi: 10.1109/TCBB.2015.2415814.
Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.
Qiu YQ, Tian X, Zhang S.
:: DESCRIPTION
Gist began as a project to develop a sequence classifier based on arbitrary input classes, and has developed into a high-precision, noise-tolerant taxonomic classifier focused specifically on the problem of annotating short (76 nt and higher), unassembled reads with little or no quality filtering
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SATIVA is a pipeline that uses Evolutionary Placement Algorithm (EPA) to identify taxonomically mislabeled sequences and suggest corrections.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Phylogeny-aware identification and correction of taxonomically mislabeled sequences.
Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A.
Nucleic Acids Res. 2016 May 10. pii: gkw396
:: DESCRIPTION
tax2tree is a tool for automatically decorating taxonomy onto a phylogenetic tree. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
Daniel McDonald, Morgan N Price, Julia Goodrich, Eric P Nawrocki, Todd Z DeSantis, Alexander Probst, Gary L Andersen, Rob Knight and Philip Hugenholtz.
ISME J. 2012 Mar;6(3):610-8. doi: 10.1038/ismej.2011.139. Epub 2011 Dec 1.
:: DESCRIPTION
TaxMan (Taxonomy database Manager) is a software package that uses freely available bioinformatics tools to allow rapid assembly, storage and analysis of large aligned DNA and protein sequence datasets for user-defined sets of species and genes. Sequence data are obtained from GenBank format files on the basis of annotation and / or sequence similarity. Consensus sequences are built and aligned automatically, and aligned sequences are stored in a database. By using the stored aligned sequences, large concatenated protein and DNA multiple sequence alignments can be rapidly generated for subsets of the dataset. Trees resulting from phylogenetic analysis can also be stored, and compared with a reference taxonomy.
::DEVELOPER
The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Martin Jones and Mark Blaxter
TaxMan: a taxonomic database manager
BMC Bioinformatics 2006, 7:536
