Metaxa2 2.2 – Identification and Classification of Small Subunit (SSU) rRNA Sequences

Metaxa2 2.2

:: DESCRIPTION

Metaxa2 is a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

::DEVELOPER

Johan Bengtsson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  Metaxa2

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2015 Mar 2. doi: 10.1111/1755-0998.12399.
metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.
Bengtsson-Palme J1, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DG, Nilsson RH.

Antonie Van Leeuwenhoek. 2011 Oct;100(3):471-5. doi: 10.1007/s10482-011-9598-6. Epub 2011 Jun 15.
Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.
Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet GA, Abarenkov K, Petri A, Rosenblad MA, Nilsson RH.

Microtaxi – Microbial Taxonomic Identification and Classification Server

Microtaxi

:: DESCRIPTION

Microtaxi uses an taxon-specific gene based approach and provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Microtaxi

:: MORE INFORMATION

Citation

BMC Genomics. 2015 May 20;16:396. doi: 10.1186/s12864-015-1542-0.
Using the taxon-specific genes for the taxonomic classification of bacterial genomes.
Gupta A, Sharma VK

CLARK 1.2.3 – Fast and Accurate Classification of Metagenomic and Genomic Sequences

CLARK 1.2.3

:: DESCRIPTION

Clark is a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed.

::DEVELOPER

Rachid OunitAlgorithms and Computational Biology Lab ,University of California

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CLARK

:: MORE INFORMATION

Citation

Ounit R, Wanamaker S, Close TJ, Lonardi S,
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
BMC Genomics 2015, 16:236.

FCP 1.0.7 – Fragment Classification Package

FCP 1.0.7

:: DESCRIPTION

FCP (Fragment classification package) is a homology- and composition-based classifiers for assigning a taxonomic attribution to metagenomic fragments.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 FCP

:: MORE INFORMATION

Citation

Parks, D.H., MacDonald, N.J., and Beiko, R.G. (2011).
Classifying short genomic fragments from novel lineages using composition and homology.
BMC Bioinformatics, 12:328.

Kraken 0.10.5-beta – Kraken Taxonomic Sequence Classification System

Kraken 0.10.5-beta

:: DESCRIPTION

Kraken is a very fast system for taxonomic classification of short or long DNA sequences from a microbiome or metagenomic sample.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Kraken

:: MORE INFORMATION

Citation

Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL.

HaploGrep 2 – Automatic mtDNA Haplogroup Classification

HaploGrep 2

:: DESCRIPTION

HaploGrep is a web application for finding the corresponding haplogroup to given mtDNA profiles based on Phylotree (mtDNA classification tree).

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

HaploGrep

:: MORE INFORMATION

Citation

HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.
Weissensteiner H, Pacher D, Kloss-Brandstätter A, Forer L, Specht G, Bandelt HJ, Kronenberg F, Salas A, Schönherr S.
Nucleic Acids Res. 2016 Apr 15. pii: gkw233

TEclass 2.1.3 – Classification of TE Consensus Sequences

TEclass 2.1.3

:: DESCRIPTION

TEclass classifies unknown transpsosable element (TE) consensus sequences into four categories, according to their mechanism of transposition: DNA transposons, LTRs, LINEs, SINEs.

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  TEclass

:: MORE INFORMATION

Citation

Abrusan G., Grundmann N., DeMeester L., Makalowski W. 2009.
TEclass: a tool for automated classification of unknown eukaryotic transposable elements.
Bioinformatics 25:1329-1330

Jstacs 2.2 – Java Framework for Statistical Analysis and Classification of Biological Sequences

Jstacs 2.2

:: DESCRIPTION

Jstacs is an open source Java library, which focuses on the statistical analysis of biological sequences instead. Jstacs comprises an efficient representation of sequence data and provides implementations of many statistical models with generative and discriminative approaches for parameter learning. Using Jstacs, classifiers can be assessed and compared on test datasets or by cross-validation experiments evaluating several performance measures.

::DEVELOPER

Jstacs Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 Jstacs

:: MORE INFORMATION

Citation

Michael Seifert, Marc Strickert, Alexander Schliep and Ivo Grosse
Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models
Bioinformatics (2011) 27 (12): 1645-1652.

CoMeta 0.3 – Classification of Metagenomes using k-mers

CoMeta 0.3

:: DESCRIPTION

CoMeta is a tool used to assigns a query read (DNA fragment) from metagenomic sample into one of the groups (the most common the taxon).

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 CoMeta

:: MORE INFORMATION

Citation

PLoS One. 2015 Apr 17;10(4):e0121453. doi: 10.1371/journal.pone.0121453. eCollection 2015.
CoMeta: classification of metagenomes using k-mers.
Kawulok J, Deorowicz S

NBC – Naive Bayes Classification tool

NBC

:: DESCRIPTION

NBC uses a method similar to that used in many email spam filters to score a genetic sample against different genomes, to possibly identify the closest match.

::DEVELOPER

Drexel’s EESI Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NBC

:: MORE INFORMATION

Citation

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads.
Rosen GL, Reichenberger ER, Rosenfeld AM.
Bioinformatics. 2011 Jan 1;27(1):127-9. doi: 10.1093/bioinformatics/btq619.

NBC update: The addition of viral and fungal databases to the Naïve Bayes classification tool.
Rosen GL, Lim TY.
BMC Res Notes. 2012 Jan 31;5:81. doi: 10.1186/1756-0500-5-81.