Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

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

The 16S ribosomal RNA gene [or 16S ribosomal DNA (rDNA)] is a commonly used marker for bacterial identification due to its universal distribution among all bacterial species and a slow rate of sequence evolution. To reduce the dimensionality of…
G T A T C G C T A
UPARSE
Desktop

UPARSE

A pipeline for constructing operational taxonomic units (OTUs) de novo from…

A pipeline for constructing operational taxonomic units (OTUs) de novo from next-generation reads that achieves high accuracy in biological sequence recovery and improves richness estimates on mock…

G T A T C G C T A
dbOTU
Desktop

dbOTU Distribution-based OTU calling

Provides an algorithm to inform the creation of OTUs for large next-generation…

Provides an algorithm to inform the creation of OTUs for large next-generation sequencing studies employing the distribution of 16S rRNA sequences. dbOTU was implemented following three different…

G T A T C G C T A
UCLUST
Desktop

UCLUST

A clustering method that exploits USEARCH to assign sequences to clusters.…

A clustering method that exploits USEARCH to assign sequences to clusters. UCLUST is superior to CD-HIT. It is usually significantly faster, uses significantly less memory, can cluster at lower…

G T A T C G C T A
CROP
Desktop

CROP Clustering 16S rRNA for OTU Prediction

Provides a clustering tool that automatically determines the best clustering…

Provides a clustering tool that automatically determines the best clustering result for 16S rRNA sequences at different phylogenetic levels. Our study shows that CROP gives accurate clustering…

G T A T C G C T A
Esprit
Web

Esprit

Estimates species richness using large collections of 16S rRNA pyrosequences.…

Estimates species richness using large collections of 16S rRNA pyrosequences. We developed two versions of ESPRIT, one for personal computers (PCs) and one for computer clusters (CCs). The PC version…

G T A T C G C T A
SUMACLUST
Desktop

SUMACLUST

Performs exact sequence alignment, rather than relying on fast heuristics.…

Performs exact sequence alignment, rather than relying on fast heuristics. SUMACLUST is a sequence-clustering application. This method is based on a strategy in which the clusters are constructed…

G T A T C G C T A
mothur
Desktop

mothur

Aims to be a comprehensive software package that allows users to use a single…

Aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. mothur builds upon previous tools to provide a flexible and…

G T A T C G C T A
RDP Classifier
Web
Desktop

RDP Classifier Ribosomal Database Project Classifier

Provides rapid taxonomic placement and summary data based on rRNA sequence…

Provides rapid taxonomic placement and summary data based on rRNA sequence data. For each high-throughput experiments, the RDP Classifier can include the number of input sequences belonging to each…

G T A T C G C T A
BEBaC
Desktop

BEBaC Bayesian Estimation of Bacterial Communities

A method for detecting bacterial communities from 454 sequencing data. Compared…

A method for detecting bacterial communities from 454 sequencing data. Compared with traditional methods, BEBaC determines the number of bacterial species automatically, while requiring no external…

G T A T C G C T A
ESPRIT-Tree
Desktop

ESPRIT-Tree

An algorithm for hierarchical clustering analysis of massive sequence data. To…

An algorithm for hierarchical clustering analysis of massive sequence data. To avoid confusion, we note that ESPRIT-Tree is not a program for determining phylogenetic trees, but rather for producing…

G T A T C G C T A
HPC-CLUST
Desktop

HPC-CLUST

A highly optimized software pipeline that can cluster large numbers of…

A highly optimized software pipeline that can cluster large numbers of pre-aligned DNA sequences by running on distributed computing hardware. HPC-CLUST allocates both memory and computing resources…

G T A T C G C T A
sl1p
Desktop

sl1p

Automates the processing of raw 16S rRNA gene sequencing data. sl1p allows…

Automates the processing of raw 16S rRNA gene sequencing data. sl1p allows users to make human-readable figures, graphs, and tables to simplify access to the collected data. This tool is developed…

G T A T C G C T A
CD-HIT-OTU
Desktop
Web

CD-HIT-OTU

Generates operational taxonomic unit (OTU) clusters for ribosomal ribonucleic…

Generates operational taxonomic unit (OTU) clusters for ribosomal ribonucleic acid (rRNA) tags from 454 and Illumina platforms. CD-HIT-OTU is a multi-step pipeline whose speed allows to cluster…

G T A T C G C T A
DNACLUST
Desktop

DNACLUST

A fast clustering tool specifically designed for clustering highly-similar DNA…

A fast clustering tool specifically designed for clustering highly-similar DNA sequences. Given a set of sequences and a sequence similarity threshold, DNACLUST creates clusters whose radius is…

G T A T C G C T A
metaxa
Desktop

metaxa

A popular utility for extracting partial rRNA sequences from large sequencing…

A popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. The…

GramDist
Desktop

GramDist

Allows users to work about clustering large data sets of 16S rDNA sequences…

Allows users to work about clustering large data sets of 16S rDNA sequences based on the inherent grammar of DNA and RNA sequences. GramDist utilizes a grammar-based distance metric to identify…

G T A T C G C T A
CLUSTOM-CLOUD
Desktop

CLUSTOM-CLOUD CLUSTering 16S NGS sequences by Overlap Minimization

A distributed clustering program that can efficiently and accurately cluster…

A distributed clustering program that can efficiently and accurately cluster 16S sequences under distributed and cloud-computing environments. CLUSTOM-CLOUD is a significant upgrade to its…

G T A T C G C T A
SigTree
Desktop

SigTree

Provides a solution to use results of operational taxonomic unit (OTU)-level…

Provides a solution to use results of operational taxonomic unit (OTU)-level significance tests to identify and visualize branches in a phylogenetic tree. SigTree permits to convert the one-sided…

G T A T C G C T A
Microclass
Desktop

Microclass

Includes some ways to quantify uncertainties in the classifications. Microclass…

Includes some ways to quantify uncertainties in the classifications. Microclass is an R package with tools for making such classifications, where the heavy computations are implemented in C++ but…

G T A T C G C T A
OTUCLUST
Desktop

OTUCLUST

Divides a set of amplicon reads into clusters. OTUCLUST is a…

Divides a set of amplicon reads into clusters. OTUCLUST is a sequence-clustering application that performs sequence dereplication and chimera removal. This method is based on a strategy in which the…

G T A T C G C T A
Swarm
Desktop

Swarm

Solves the problems of arbitrary global clustering thresholds and centroid…

Solves the problems of arbitrary global clustering thresholds and centroid selection induced input-order dependency, and creates robust and more natural Operational Taxonomic Units (OTUs) than…

G T A T C G C T A
MetaPhyl
Desktop

MetaPhyl

A classification method for 16S rDNA sequence samples that uses the natural…

A classification method for 16S rDNA sequence samples that uses the natural structure of microbial community data encoded by a phylogenetic tree. We showed that using the phylogenetic information…

G T A T C G C T A
FUNGuild
Dataset

FUNGuild Fungi fUNctional Guild

Used to taxonomically parse fungal operational taxonomic units (OTUs) by…

Used to taxonomically parse fungal operational taxonomic units (OTUs) by ecological guild independent of sequencing platform or analysis pipeline. FUNGuild is a two-component tool consisting of a…

G T A T C G C T A
SSUnique
Desktop

SSUnique

Filters unclassified and/or rare operational taxonomic units from 16S rRNA gene…

Filters unclassified and/or rare operational taxonomic units from 16S rRNA gene sequence libraries by screening against consensus structural models for small-subunit (SSU) rRNA. SSUnique promotes the…

G T A T C G C T A
oclust
Desktop

oclust

Clusters long 16S rRNA sequencing reads, or any sequences, into Operational…

Clusters long 16S rRNA sequencing reads, or any sequences, into Operational Taxonomic Units. oclust permits the reduction of computational footprint (sequences can be aligned within reasonable time…

G T A T C G C T A
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…

G T A T C G C T A
DBH
Desktop

DBH

Infers Operational Taxonomic Units (OTUs) from massive 16S rRNA sequences with…

Infers Operational Taxonomic Units (OTUs) from massive 16S rRNA sequences with high accuracy and low computational complexity. DBH is a clustering method that consists of two distinct elements: (i)…

G T A T C G C T A
NINJA-OPS
Desktop

NINJA-OPS NINJA Is Not Just Another - OTU Picking Solution

Takes advantage of the Burrows-Wheeler (BW) alignment using an artificial…

Takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the “concatesome” as the BW input. NINJA-OPS also…

G T A T C G C T A
DySC
Desktop

DySC Dynamic Seed-based Clustering

A scalable tool for clustering of 16S rRNA reads for microbial profiling…

A scalable tool for clustering of 16S rRNA reads for microbial profiling generated by high-throughput sequencing machines, which can cluster millions of reads on a standard workstation within a few…

G T A T C G C T A
Piphillin
Web

Piphillin

Predicts metagenomes with high accuracy by leveraging the most-current genome…

Predicts metagenomes with high accuracy by leveraging the most-current genome reference databases. Piphillin uses direct nearest-neighbor matching between 16S rRNA amplicons and genomes to predict…

G T A T C G C T A
MTV-LMM
Algorithm

MTV-LMM Microbial community Temporal Variability Linear Mixed Model

Helps quantify the dependency of operational taxonomic units (OTUs) on past…

Helps quantify the dependency of operational taxonomic units (OTUs) on past occurrences. MTV-LMM is an algorithm developed to detect temporal dependencies. It also has the ability to quantify the…

G T A T C G C T A
Ananke
Desktop

Ananke

Clusters sequences based on temporal dynamics rather than sequence identity.…

Clusters sequences based on temporal dynamics rather than sequence identity. Ananke aims to group unique marker-gene sequences that are ‘‘dynamically similar’’. It complements traditional…

G T A T C G C T A
MeShClust
Desktop

MeShClust

Calculates sequence similarity. MeShClust utilizes an instance of unsupervised…

Calculates sequence similarity. MeShClust utilizes an instance of unsupervised machine learning algorithms to cluster DNA sequences. It is capable of correcting the provided identity score to a great…

G T A T C G C T A
DMclust
Desktop

DMclust

Achieves higher clustering quality with relative lower time complexity compared…

Achieves higher clustering quality with relative lower time complexity compared with similar methods. DMclust is a density-based modularity clustering method developed for Operational Taxonomic Units…

G T A T C G C T A
PhyloToAST
Desktop

PhyloToAST Phylogenetic Tools for Analysis of Species-level Taxa

Distributes BLAST-based OTU picking across computing clusters. PhyloToAST…

Distributes BLAST-based OTU picking across computing clusters. PhyloToAST provides several improved/new visualization methods, tools for filtering and sub-setting results files, simple name lookup…

G T A T C G C T A
ESPRIT-Forest
Desktop

ESPRIT-Forest

Performs parallel hierarchical clustering of sequences. ESPRIT-Forest is…

Performs parallel hierarchical clustering of sequences. ESPRIT-Forest is algorithm with a cluster version. The software inherits the same pipeline of ESPRIT and ESPRIT-Tree, which performs…

G T A T C G C T A
MAPseq
Desktop

MAPseq

Classifies ribosomal RNA sequences in terms of their taxonomy and operational…

Classifies ribosomal RNA sequences in terms of their taxonomy and operational taxonomic unit (OTU) classification. MAPseq uses a reference set of full-length ribosomal RNA sequences for which known…

G T A T C G C T A
Deblur
Desktop

Deblur

Uses error profiles to obtain putative error-free sequences from Illumina MiSeq…

Uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms. Deblur reduces computational demands relative to similar sub-operational-taxonomic-unit…

G T A T C G C T A
MetaDP
Web

MetaDP

Provides pre-defined workflows for metagenomic data analysis and disease…

Provides pre-defined workflows for metagenomic data analysis and disease prediction modeling based on the Galaxy platform. MetaDP is an automated software for 16S rRNA sequencing data analysis,…

G T A T C G C T A
MICCA
Desktop

MICCA MICrobial Community Analysis

Provides accurate results reaching a good compromise among modularity and…

Provides accurate results reaching a good compromise among modularity and usability. MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality…

G T A T C G C T A
DBC
Desktop

DBC Distribution-based clustering

Allows users to group DNA sequences. DBC is an algorithm developed mainly for…

Allows users to group DNA sequences. DBC is an algorithm developed mainly for Illumina next-generation sequencing libraries but can be used with any sequencing platforms. It accommodates differences…

G T A T C G C T A
MetAmp
Desktop

MetAmp

A method and corresponding application to combine amplicon data from multiple…

A method and corresponding application to combine amplicon data from multiple genomic markers into Operational Taxonomic Units (OTUs) for microbial community analysis, calibrating the markers using…

G T A T C G C T A
LOTUS
Desktop

LOTUS less operational taxonomic units scripts

Calculates denoised, chimera-checked, operational taxonomic units (OTUs). LOTUS…

Calculates denoised, chimera-checked, operational taxonomic units (OTUs). LOTUS analyses microbial 16S data with comparable or even better results than existing pipelines, requiring a fraction of the…

G T A T C G C T A
GramCluster
Desktop

GramCluster

A fast and accurate algorithm for clustering large data sets of 16S rDNA…

A fast and accurate algorithm for clustering large data sets of 16S rDNA sequences based on the inherent grammar of DNA and RNA sequences. Lempel-Ziv parsing is used to estimate the grammar of each…

G T A T C G C T A
bioOTU
Desktop

bioOTU

Calculates simultaneous taxonomic assignments and Operational Taxonomic Units…

Calculates simultaneous taxonomic assignments and Operational Taxonomic Units (OTUs) clustering of 16s rRNA gene sequences. bioOTU is specifically designed for first assigning taxonomy to tags at…

G T A T C G C T A
M-pick
Desktop

M-pick

A modularity-based clustering method, for operational taxonomic unit (OTU)…

A modularity-based clustering method, for operational taxonomic unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off value, and our simulation studies…

G T A T C G C T A
16S Classifier
Desktop
Web

16S Classifier

A Random Forest based tool which is developed to carry out fast, efficient and…

A Random Forest based tool which is developed to carry out fast, efficient and accurate taxonomic classification of 16S rRNA sequences. 16S Classifier has the unique ability to classify small…

G T A T C G C T A
OptiClust
Desktop

OptiClust

Optimizes the Matthews correlation coefficient, a measure of the quality of…

Optimizes the Matthews correlation coefficient, a measure of the quality of operational taxonomic unit assignments. OptiClust produces more robust assignments and does so in a rapid and memory…

G T A T C G C T A
UniFrac
Desktop

UniFrac

Measures the phylogenetic distance between sets of taxa in a phylogenetic tree…

Measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but…

G T A T C G C T A
EstS
Desktop

EstS EstimateS

Combines biodiversity statistics, estimators, and indices based on biotic…

Combines biodiversity statistics, estimators, and indices based on biotic sampling data. EstS is able to compute (1) expected species accumulation curves for rarefied reference samples, (2) expected…

G T A T C G C T A
DOTUR
Desktop

DOTUR Distance based OTU and Richness determination

Assigns sequences to OTUs (operational taxonomic units) by using either the…

Assigns sequences to OTUs (operational taxonomic units) by using either the furthest, average, or nearest neighbor algorithm for each distance level. DOTUR uses the frequency at which each OTU is…

G T A T C G C T A
microPITA
Desktop

microPITA microbiomes: Picking Interesting Taxonomic Abundance

Picks interesting taxonomic abundance. microPITA is a computational tool…

Picks interesting taxonomic abundance. microPITA is a computational tool enabling sample selection in two-stage (tiered) studies. Using two-stage designs can more efficiently allocate resources,…

G T A T C G C T A
MSClust
Desktop

MSClust Multi-Seeds based Clustering algorithm

An adaptive multi-seeds based heuristic clustering method that avoids the large…

An adaptive multi-seeds based heuristic clustering method that avoids the large memory need for storing seeds and/or distance matrix. MSClust uses a greedy heuristic strategy to build one cluster at…

G T A T C G C T A
Taxonerator
Desktop

Taxonerator

Carries out simple similarity-based annotation of clustered barcode sequence…

Carries out simple similarity-based annotation of clustered barcode sequence data produced by jMOTU. Taxonerator generates taxonomic annotation for MOTU by BLASTing representative sequences against a…

G T A T C G C T A
jMOTU
Desktop

jMOTU

Analyses DNA barcode datasets. jMOTU uses an explicit and determinated…

Analyses DNA barcode datasets. jMOTU uses an explicit and determinated algorithm to define molecular operational taxonomic units. It is useful for both individual specimen-based Sanger sequencing…

G T A T C G C T A
BOTUX
Desktop

BOTUX Bayesian-like Operational Taxonomic Unit Examiner

Performs clustering with high precision. BOTUX is an Operational Taxonomic Unit…

Performs clustering with high precision. BOTUX is an Operational Taxonomic Unit (OTU) assignment method. It has been extended to single-end and paired-end Illumina datasets and performs acceptably at…

G T A T C G C T A
TAXAassign
Desktop

TAXAassign

Attributes taxonomic assignments to nucleotide sequences at different levels by…

Attributes taxonomic assignments to nucleotide sequences at different levels by using NCBI's Taxonomy. TAXAassign also provides taxa abundances for a given set of sequences which can be gathered…

ParsInsert
Desktop

ParsInsert

Proposes a Parsimonious Insertion’ algorithm implementation. ParsInsert…

Proposes a Parsimonious Insertion’ algorithm implementation. ParsInsert allows users to explore information derived from publicly available curated phylogenetic trees with the aims of add new…

G T A T C G C T A
EMDUnifrac
Desktop

EMDUnifrac Earth Movers Distance Unifrac

Computes the Unifrac distance and also returns the differentially abundant…

Computes the Unifrac distance and also returns the differentially abundant operational taxonomic units (OTUs) that contributed to this distance. EMDUnifrac is based on a linear time algorithm. It can…

G T A T C G C T A
TreeChopper
Desktop

TreeChopper

Allows to assemble tree leaf nodes in accordance with the phylogenetic…

Allows to assemble tree leaf nodes in accordance with the phylogenetic distance. TreeChopper permits to construct a graph and examine every edge connecting pairs of nodes. This tool gives access to…

G T A T C G C T A
Otupipe
Desktop

Otupipe

Creates operational taxonomic units (OTUs) from next-generation sequence reads…

Creates operational taxonomic units (OTUs) from next-generation sequence reads for single-region experiments such as 16S and ITS. Otupipe is a bash script. It requires two arguments: an input file in…

G T A T C G C T A
Fast Unifrac
Web

Fast Unifrac

Allows analysis of large phylogenetic datasets. Fast Unifrac facilitates rapid…

Allows analysis of large phylogenetic datasets. Fast Unifrac facilitates rapid identification of patterns in large and complex datasets. It permits to expand insight into a wide range of microbial…

G T A T C G C T A
MtHc
Desktop

MtHc

Achieves higher cluster quality and lower time complexity for millions of 16S…

Achieves higher cluster quality and lower time complexity for millions of 16S rRNA sequences. MtHc is a motif-based hierarchical method for clustering massive rRNA sequences into Operational…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.