tax2tree 1.0 – Decorating Taxonomy onto a Phylogenetic tree

tax2tree 1.0

:: 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

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python
  • PyCogent

:: DOWNLOAD

 tax2tree

:: 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.

SATIVA 0.9 – Semi-Automatic Taxonomy Improvement and Validation Algorithm

SATIVA 0.9

:: DESCRIPTION

SATIVA is a pipeline that uses Evolutionary Placement Algorithm (EPA) to identify taxonomically mislabeled sequences and suggest corrections.

::DEVELOPER

Alexey Kozlov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 SATIVA

:: 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

HTTMM – Hierarchical Taxonomy Tree based Mixture Model

HTTMM

:: 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

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 HTTMM

:: 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.

RDP Classifier 2.11 – Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

RDP Classifier 2.11

:: 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

  • Linux / Mac OsX /Windows
  • Java

:: DOWNLOAD

 RDP Classifier

:: 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.

Gist 0.6.04b – Generative Inference of Sequence Taxonomy

Gist 0.6.04b

:: 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

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Gist

:: MORE INFORMATION

TreeMaker 1.3 – Interactive Building of Taxonomies

TreeMaker 1.3

:: 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

  • Windows / MacOsX / Linux

:: DOWNLOAD

 TreeMaker

:: 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.

IM-TORNADO 2.0.3.2 – Illinois Mayo Taxonomy Operations for RNA Database Operations

IM-TORNADO 2.0.3.2

:: DESCRIPTION

IM-TORNADO is a pipeline for analysis of paired-end 16S rDNA amplicon data.

::DEVELOPER

IM-TORNADO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IM-TORNADO

:: 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.

TaxMan 1.1 – Taxonomy Database Manager

TaxMan 1.1

:: 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

TaxMan

:: MORE INFORMATION

Citation:

Martin Jones and Mark Blaxter
TaxMan: a taxonomic database manager
BMC Bioinformatics 2006, 7:536