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Homology-based taxonomic classification software tools | 16S ribosomal RNA sequencing data analysis

The taxonomic classification of environmental 16S rRNA gene sequences is carried out by using either a homology-based or prediction-based approach. The former approach requires the alignment of a query 16S rRNA sequence with all the 16S rRNA…
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RDP
Web
Desktop

RDP Ribosomal Database Project

Provides aligned and annotated ribosomal RNA (rRNA) gene sequence data, along…

Provides aligned and annotated ribosomal RNA (rRNA) gene sequence data, along with tools to allow researchers to analyse their own rRNA gene sequences. RDP offers tools for browsing and searching the…

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Vikodak
Web

Vikodak

A multi-modular package that is based on the above assumption and automates…

A multi-modular package that is based on the above assumption and automates inferring and/ or comparing the functional characteristics of an environment using taxonomic abundance generated from one…

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Karp
Desktop

Karp

Identifies the relative frequencies of reference sequences contributing to a…

Identifies the relative frequencies of reference sequences contributing to a pooled DNA sample. Karp combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood…

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SINA
Web

SINA SILVA Incremental Aligner

Aligns and optionally taxonomically classifies ribosomal RNA (rRNA gene…

Aligns and optionally taxonomically classifies ribosomal RNA (rRNA gene sequences). SINA is part of the rRNA gene processing pipeline of the SILVA ribosomal databases project. The software can…

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TANGO
Desktop

TANGO

Provides taxonomic assignment a metagenomic dataset. TANGO classifies sequence…

Provides taxonomic assignment a metagenomic dataset. TANGO classifies sequence reads according to their most probable taxonomic rank starting from a reference taxonomy and a set of sequence read…

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Taxonomer
Web

Taxonomer

An ultrafast web-tool for comprehensive metagenomics data analysis and…

An ultrafast web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and…

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Greengenes
Web

Greengenes

Provides quality-controlled microbial DNA data and tools to researchers for…

Provides quality-controlled microbial DNA data and tools to researchers for rapid analysis of user-generated sequences.

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GASiC
Desktop

GASiC Genome Abundance Similarity Correction

A method to correct read alignment results for the ambiguities imposed by…

A method to correct read alignment results for the ambiguities imposed by similarities of genomes.

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AmosCmp16Spipel…
Desktop

AmosCmp16Spipeline

Uses the AMOScmp software to assemble multiple, potentially overlapping 16S…

Uses the AMOScmp software to assemble multiple, potentially overlapping 16S rRNA sequencing reads based on read mappings to a reference 16S rRNA gene. AmosCmp16Spipeline is a sequence assembly. An…

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RiboFR-Seq
Desktop

RiboFR-Seq Ribosomal RNA gene flanking region sequencing

A method for capturing both ribosomal RNA variable regions and their flanking…

A method for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. This approach goes beyond traditional metagenomic analysis by taking into account…

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Calypso
Desktop

Calypso

Enables quantitative visualizations, statistical testing, multivariate…

Enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Calypso is…

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BLCA
Desktop

BLCA Bayesian Lowest Common Ancestor

Calculates true sequence similarity between query sequences and database hits…

Calculates true sequence similarity between query sequences and database hits using pairwise sequence alignment. BLCA is based on a Bayesian Lowest Common Ancestor (LCA) method. It is able to perform…

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ECOMICS
Web

ECOMICS ECosystem trans-OMICS investigation

Provides a suite for trans-omics approaches. ECOMICS is composed of four…

Provides a suite for trans-omics approaches. ECOMICS is composed of four components: (i) E-class, for taxonomic classification of prokaryotic and eukaryotic DNA sequences, (ii) FT2B to process…

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BROCC
Desktop

BROCC BLAST Read and Operational Taxonomic Unit Consensus Classifier

Provides a well-characterized tool kit for sequence-based enumeration of…

Provides a well-characterized tool kit for sequence-based enumeration of eukaryotic organisms in human microbiome samples. BROCC is a pipeline for attributing sequences that was tailored for use with…

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TUIT
Desktop

TUIT Taxonomic Unit Identification Tool

An efficient open source and platform-independent application that can perform…

An efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic…

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ARK
Desktop

ARK Aggregation of Reads by K-means

A software package for estimation of bacterial community composition. ARK is…

A software package for estimation of bacterial community composition. ARK is based on a statistical argument via mixture density formulation. The community composition estimates can be substantially…

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SINTAX
Algorithm

SINTAX SImple Non-Bayesian TAXonomy

Predicts taxonomy using the similarity of k-mer to determine the best result in…

Predicts taxonomy using the similarity of k-mer to determine the best result in a reference database. SINTAX is an algorithm that operates in two steps: (i) it finds the top k-mer hit and (ii) the…

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MALT
Desktop

MALT MEGAN alignment tool

Aligns and analyzes metagenomic DNA sequencing data. MALT is based on a…

Aligns and analyzes metagenomic DNA sequencing data. MALT is based on a taxonomic binning algorithm that can assign reads to bacterial species. Applied to ancient microbiomes from oral cavity and…

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SEK
Desktop

SEK Sparsity Exploiting K-mer

An approach where the estimation of the bacterial community composition is…

An approach where the estimation of the bacterial community composition is performed jointly. SEK is based on kernel density estimators and mixture density models, and it leads to solving an…

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SPINGO
Desktop

SPINGO SPecies level IdentificatioN of metaGenOmic amplicons

A rapid, accurate and flexible classifier that improves the taxonomic…

A rapid, accurate and flexible classifier that improves the taxonomic resolution of 16S rRNA gene amplicons down to species level. While its primary target is species from any type of environmental…

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SONS
Desktop

SONS Shared OTUs and Similarity

Determines the abundance distribution of OTUs that are either endemic to or…

Determines the abundance distribution of OTUs that are either endemic to or shared between samples. SONS is a versatile and powerful tool that will complement the suite of tools used by microbial…

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SequenceServer
Desktop

SequenceServer

A modern graphical user interface for custom BLAST databases. SequenceServer…

A modern graphical user interface for custom BLAST databases. SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally and for sharing with colleagues…

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PyNAST
Desktop

PyNAST Python Nearest Alignment Space Termination

Uses as a flexible tool for aligning sequences to a template alignment. PyNAST…

Uses as a flexible tool for aligning sequences to a template alignment. PyNAST is a reimplementation of NAST (Nearest Alignment Space Termination), introducing new features that increase its…

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Taxy
Desktop

Taxy

A method for taxonomic profiling based on mixture modeling of the overall…

A method for taxonomic profiling based on mixture modeling of the overall oligonucleotide distribution of a sample. The main advantage of the Taxy approach over all existing methods is the inherent…

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Taxy-Pro
Desktop

Taxy-Pro

In contrast to the oligonucleotide-based Taxy method, Taxy-Pro is based on…

In contrast to the oligonucleotide-based Taxy method, Taxy-Pro is based on mixture model analysis of protein signatures in terms of protein domain frequencies. The Pfam domain counts of a metagenome…

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Quikr
Desktop

Quikr QUadratic, K-mer–based, Iterative, Reconstruction method

Computes a vector of taxonomic assignments and their proportions in the sample…

Computes a vector of taxonomic assignments and their proportions in the sample using an optimization technique motivated from the mathematical theory of compressive sensing. On both simulated and…

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MetaSAMS
Web

MetaSAMS

A software platform for automated taxonomic and functional analysis of…

A software platform for automated taxonomic and functional analysis of metagenome data. MetaSAMS includes a pipeline consisting of three different classifiers that perform taxonomic profiling of…

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C16S
Web

C16S

An algorithm for taxonomic classification of 16S rDNA fragments. The C16S…

An algorithm for taxonomic classification of 16S rDNA fragments. The C16S algorithm adopts a two phase approach for the taxonomic classification of partial or full-length 16S rDNA sequences. First,…

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TaxAss
Desktop

TaxAss

Produces fine level taxonomy classifications. TaxAss is based on an…

Produces fine level taxonomy classifications. TaxAss is based on an ecosystem-specific database and a comprehensive database to maintain the full biological diversity, taxonomic richness and accuracy…

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S-LIBSHUFF
Desktop

S-LIBSHUFF

Uses the exact and integral form of the Cramer-von Mises statistic. S-LIBSHUFF…

Uses the exact and integral form of the Cramer-von Mises statistic. S-LIBSHUFF analyzes more than two libraries with a single input file and single execution of the program, measures the probability…

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