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Taxonomy-dependent methods (shotgun metagenomic analysis)

A majority of methods available for binning datasets obtained using shotgun sequencing belong to the taxonomy-dependent category. Based on the strategy used for comparing reads with sequences/pre-computed models, taxonomy-dependent methods can be…
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MetaPhlAn
Desktop

MetaPhlAn Metagenomic Phylogenetic Analysis

Estimates the relative abundance of microbial cells by mapping reads against a…

Estimates the relative abundance of microbial cells by mapping reads against a reduced set of clade-specific marker sequences. MetaPhlAn accurately profiles microbial communities and requires only…

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PhymmBL
Desktop

PhymmBL

A classification system designed for metagenomics experiments that assigns…

A classification system designed for metagenomics experiments that assigns taxonomic labels to short DNA reads. PhymmBL combines two components: (i) composition-directed taxonomic predictions from…

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MEGAN
Desktop

MEGAN MEtaGenome ANalyzer

Allows to interactively explore and analyze, both taxonomically and…

Allows to interactively explore and analyze, both taxonomically and functionally, large-scale microbiome sequencing data. MEGAN is a comprehensive microbiome analysis toolbox for metagenome,…

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AMPHORA
Web
Desktop

AMPHORA AutoMated PHylogenomic infeRence Application

Allows genome tree reconstruction and metagenomic phylotyping. AMPHORA is an…

Allows genome tree reconstruction and metagenomic phylotyping. AMPHORA is an application for large-scale protein phylogenetic analysis. The software supports the analyses of DNA sequences, which…

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Pyrotools
Desktop

Pyrotools

Represents the consensus sequences in a region of interest (ROI). Pyrotools is…

Represents the consensus sequences in a region of interest (ROI). Pyrotools is based on the graph technique that resembles the partial order graph or variant graph. It can model error patterns in the…

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Centrifuge
Desktop

Centrifuge

A rapid and sensitive classifier for microbial sequences with low memory…

A rapid and sensitive classifier for microbial sequences with low memory requirements and a speed comparable to the fastest systems. The system uses an indexing scheme based on the Burrows-Wheeler…

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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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mOTU
Desktop

mOTU

A method that uses a subset of marker genes (MGs) for taxonomic profiling of…

A method that uses a subset of marker genes (MGs) for taxonomic profiling of metagenomes. mOTU is available as a standalone software and is also implemented in MOCAT. Species-level profiles are…

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SATIVA
Desktop

SATIVA Semi-Automatic Taxonomy Improvement and Validation Algorithm

A phylogeny-aware method to automatically identify taxonomically mislabeled…

A phylogeny-aware method to automatically identify taxonomically mislabeled sequences (mislabels) using statistical models of evolution. SATIVA use the Evolutionary Placement Algorithm (EPA) to…

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CARMA
Desktop
Web

CARMA

A software pipeline for characterizing the taxonomic composition and genetic…

A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes.

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Treephyler
Desktop

Treephyler

A package for fast taxonomic profiling of metagenomes. Treephyler combines the…

A package for fast taxonomic profiling of metagenomes. Treephyler combines the predictive power of tree-based and speed of signature-based approaches. It was evaluated on real metagenome to assess…

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MGmapper
Desktop

MGmapper

Simplifies the processing of next generation sequences from biological samples.…

Simplifies the processing of next generation sequences from biological samples. MGmapper provides an access for routine analysis of complex datasets, enabling usage of many whole genome reference…

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CSSSCL
Desktop

CSSSCL Combined Sequence Similarity Score CLassifier

A Python package to facilitate the accurate taxonomic classification of long…

A Python package to facilitate the accurate taxonomic classification of long and short DNA sequences. For the purpose of validation, and to demonstrate its usefulness we test the combined sequence…

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Kaiju
Desktop
Web

Kaiju

A program for the taxonomic classification of metagenomic high-throughput…

A program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database…

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TaxSOM
Desktop

TaxSOM

A tool for taxonomic classification of DNA fragments, as they are typically…

A tool for taxonomic classification of DNA fragments, as they are typically obtained in metagenome projects.

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WebMGA
Desktop
Web

WebMGA

A customizable web server for fast metagenomic analysis. WebMGA includes over…

A customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing…

MG-RAST
Dataset

MG-RAST

An open-submission data portal for processing, analyzing, sharing and…

An open-submission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. The system currently hosts over 200,000 datasets and is continuously updated. The volume of…

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Pplacer
Desktop

Pplacer

Places query sequences on a fixed reference phylogenetic tree to maximize…

Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.

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k-SLAM
Desktop

k-SLAM k-mer Sorted List Alignment and Metagenomics

A metagenomic classifier for the characterization of metagenomic data. k-SLAM…

A metagenomic classifier for the characterization of metagenomic data. k-SLAM uses a k-mer method to rapidly produce alignments of the reads against a database and can therefore find genes and…

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MetaPhyler
Desktop

MetaPhyler

A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic…

A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference.

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LMAT
Desktop

LMAT Livermore Metagenomics Analysis Toolkit

A method presented to shift computational costs to an offline computation by…

A method presented to shift computational costs to an offline computation by creating a taxonomy/genome index that supports scalable metagenomic classification. LMAT is designed to efficiently assign…

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Binning_refiner
Desktop

Binning_refiner

Improves genome bins through the combination of different binning programs.…

Improves genome bins through the combination of different binning programs. Binning_refiner can significantly reduce the contamination level of genome bins and increase the total size of…

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PPS+
Desktop

PPS+ PhyloPythiaS+

A taxonomic assignment program that produces accurate assignments with a…

A taxonomic assignment program that produces accurate assignments with a precision of 80% or more also for low-ranking taxa from metagenome samples. PPS+ is a fully automated successor of the…

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MLTreeMap
Web

MLTreeMap

Analyzes DNA sequences and determines their most likely phylogenetic origin.

Analyzes DNA sequences and determines their most likely phylogenetic origin.

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TACOA
Desktop

TACOA

Software that can accurately predict the taxonomic origin of genomic fragments…

Software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function.

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GOTTCHA
Desktop

GOTTCHA Genomic Origins Through Taxonomic CHAllenge

A gene-independent and signature-based metagenomic taxonomic profiling method…

A gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller false discovery rates (FDR) than any other available method. GOTTCHA uses…

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deSPI
Desktop

deSPI

A metagenomic read classification method, which has higher speed and affordable…

A metagenomic read classification method, which has higher speed and affordable memory cost with higher or equal sensitivity and accuracy. deSPI recognizes and analyzes the short-token matches…

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MBMC
Desktop

MBMC Metagenomic Binning by Markov Chains

Bins reads from unknown species. MBMC measures the similarity of reads to the…

Bins reads from unknown species. MBMC measures the similarity of reads to the trained Markov chains for different taxa contrary to other approach that directly compares reads with known genomic…

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TIPP
Desktop

TIPP Taxon Identification and Phylogenetic Profiling

A marker-based method developed for abundance profiling of metagenomic data.…

A marker-based method developed for abundance profiling of metagenomic data. TIPP combines SATé-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control…

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LCAStar
Desktop

LCAStar

Assigns taxonomy to contigs assembled from environmental sequence information…

Assigns taxonomy to contigs assembled from environmental sequence information using the NCBI Tree. LCA* identifies a sufficiently strong majority on the hierarchy while minimizing entropy changes to…

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PROTAX
Desktop

PROTAX

A probabilistic method for taxonomical classification of DNA sequences. Given a…

A probabilistic method for taxonomical classification of DNA sequences. Given a pre-defined taxonomical tree structure that is partially populated by reference sequences, PROTAX decomposes the…

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Large scale…
Desktop

Large scale metagenomics

A rank-flexible compositional approach trained with large-scale machine…

A rank-flexible compositional approach trained with large-scale machine learning methods and assess its performance in different situations. It provides an interesting trade-off in speed and accuracy…

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DUDes
Desktop

DUDes

A reference-based taxonomic profiler that introduces a novel top-down approach…

A reference-based taxonomic profiler that introduces a novel top-down approach to analyze metagenomic NGS samples. Rather than predicting an organism presence in the sample based only on relative…

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cuCLARK
Desktop

cuCLARK

Provides similar functionality and usability to CLARK. cuCLARK is a hybrid…

Provides similar functionality and usability to CLARK. cuCLARK is a hybrid metagenomic read classifier executed on multi-core CPU and massively parallel GPUs. It can assign taxonomic labels at the…

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PPS
Web

PPS PhyloPythiaS

A web server for the taxonomic assignment of metagenome sequences. PhyloPythiaS…

A web server for the taxonomic assignment of metagenome sequences. PhyloPythiaS is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between…

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Kraken
Desktop

Kraken

A system for assigning taxonomic labels to short DNA sequences, usually…

A system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

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MARTA
Desktop

MARTA Metagenomic AND rDNA Taxonomic Assignment

A suite of Java-based software to better provide taxonomic assignments to DNA…

A suite of Java-based software to better provide taxonomic assignments to DNA sequences. MARTA is useful for protistologists, virologists, mycologists and other microbial ecologists. The program…

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CLARK
Desktop

CLARK CLAssifier based on Reduced K-mers

An approach to classify metagenomic reads at the species or genus level with…

An approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification…

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RAIphy
Desktop

RAIphy

Classifies and taxonomically labels metagenomic fragment. RALphy is a…

Classifies and taxonomically labels metagenomic fragment. RALphy is a semi-supervised metagenomic fragment classification program that exploits inherent features of genomic signatures with a measure…

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LikelyBin
Desktop

LikelyBin

Allows to cluster sequences with high accuracy. LikelyBin is based on k-mer…

Allows to cluster sequences with high accuracy. LikelyBin is based on k-mer distributions and uses a Markov Chain Monte Carlo (MCMC) framework. It estimates the set of master distributions and…

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Genometa
Desktop

Genometa

A Java based local bioinformatics program which allows rapid analysis of…

A Java based local bioinformatics program which allows rapid analysis of metagenomic short read datasets.

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GSMer
Desktop

GSMer

Devotes to identify genome-specific markers (GSMs) from currently sequenced…

Devotes to identify genome-specific markers (GSMs) from currently sequenced microbial genomes using a k-mer based approach. Explored GSMs could be used to identify microbial strains/species in…

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MyTaxa
Desktop
Web

MyTaxa

A homology-based bioinformatics framework to classify metagenomic and genomic…

A homology-based bioinformatics framework to classify metagenomic and genomic sequences.

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WEVOTE
Desktop

WEVOTE WEighted VOting Taxonomic idEntification

Classifies metagenome shotgun sequencing DNA reads based on an ensemble of…

Classifies metagenome shotgun sequencing DNA reads based on an ensemble of existing methods using k-mer-based, marker-based, and naive-similarity based approaches. WEVOTE is an efficient and…

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ICTV
Dataset

ICTV International Committee on Taxonomy of Viruses

Provides access to taxonomy database of virus. ICTV permits the access of an…

Provides access to taxonomy database of virus. ICTV permits the access of an online resource that offers an extensive collection of information supporting its overall activities, including the ICTV…

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MetaCache
Desktop

MetaCache

Indexes data structure and reads classification. MetaCache advances the…

Indexes data structure and reads classification. MetaCache advances the state-of-the-art in k-mer based read classification approaches. It uses minhashing only a subset of k-mers, reducing the size…

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MetaOthello
Desktop

MetaOthello

Leverages a novel probabilistic hashing structure, l-Othello, to conduct…

Leverages a novel probabilistic hashing structure, l-Othello, to conduct taxonomic classification using taxon specific k-mer signatures. MetaOthello is a metagenomic sequencing read classifier that…

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SMURF
Desktop

SMURF Short MUltiple Regions Framework

Enables identification of near full-length 16S rRNA gene sequences in microbial…

Enables identification of near full-length 16S rRNA gene sequences in microbial communities. SMURF may be applied to standard sample preparation protocols with very little modifications. It also…

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Opal
Desktop

Opal

Allows to identify the origin species of DNA sequencing reads. The Opal method…

Allows to identify the origin species of DNA sequencing reads. The Opal method introduces low-density and tries to do quick and accurate metagenomic binning. This method is a dimensionality reduction…

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MetaAmp
Web

MetaAmp

Serves for processing of small subunit (SSU) rRNA gene and other non-coding or…

Serves for processing of small subunit (SSU) rRNA gene and other non-coding or protein-coding amplicon sequencing data. MetaAmp contains merging of forward, read quality control, and reverse reads of…

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taxMaps
Desktop

taxMaps

Maps taxonomic short-read data. taxMaps is designed to deal with large DNA/RNA…

Maps taxonomic short-read data. taxMaps is designed to deal with large DNA/RNA metagenomics data. It can prioritize mapping to multiple indexes, detail mapping reports and offers interactive results…

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FHiTINGS
Desktop
MicrobiomeAnaly…
Web

MicrobiomeAnalyst

Integrates recent progress in statistics and visualization techniques.…

Integrates recent progress in statistics and visualization techniques. MicrobiomeAnalyst provides an analysis of common data outputs produced from microbiome studies. It gives support for diversity…

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GSM
Desktop

GSM Genome-Specific Markers

Allows user to profile microbial genomes in the community using Genomic…

Allows user to profile microbial genomes in the community using Genomic Specific Markers (GSM). GSM is a composition-based approach that uses GSM of reference genomes to build an index for efficient…

MIPE
Desktop

MIPE MIcrobiota Prior knowledge Explorer

Combines automated small subunit (SSU) primer evaluation with rRNA gene…

Combines automated small subunit (SSU) primer evaluation with rRNA gene extraction and classification for the analysis of shotgun metagenomic and metatranscriptomic datasets. MIPE is a metagenome…

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MetaShot
Desktop

MetaShot Metagenomics Shotgun

Assesses the total microbiome composition from host-associated shotgun sequence…

Assesses the total microbiome composition from host-associated shotgun sequence data. MetaShot shows its overall optimal accuracy performance by analyzing both simulated and real datasets. It…

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ClaMS
Desktop

ClaMS Classifier for Metagenomic Sequences

Allows to bin assembled contigs in metagenomes. ClaMS is a sequence…

Allows to bin assembled contigs in metagenomes. ClaMS is a sequence composition-based classifier targeted for use on assembled contigs with supervision from the user and in this scenario. Precomputed…

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spaced-seeds-fo…
Desktop

spaced-seeds-for-metagenomics

This general framework shows that spaced seeds provide a significant…

This general framework shows that spaced seeds provide a significant improvement of classification accuracy, as opposed to traditional contiguous k-mers. This thesis is supported through a series of…

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Taxator-tk
Desktop

Taxator-tk

Performs taxonomic sequence assignment by fast approximate determination of…

Performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Taxator-tk was precise in its taxonomic assignment across all ranks and…

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MetaCRAM
Desktop

MetaCRAM

A de novo, parallelized software suite specialized for FASTA and FASTQ format…

A de novo, parallelized software suite specialized for FASTA and FASTQ format metagenomic read processing and lossless compression. MetaCRAM integrates algorithms for taxonomy identification and…

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SeMeta
Desktop

SeMeta

A taxonomic assignment algorithm based on semi-supervised learning to produce a…

A taxonomic assignment algorithm based on semi-supervised learning to produce a fast and highly accurate classification of short-length reads with sufficient mutual overlap. SeMeta firstly separates…

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AKE
Web

AKE Accelerated K-mer Explorer

Allows rapid taxonomic assignment with small and adaptive data models. AKE is…

Allows rapid taxonomic assignment with small and adaptive data models. AKE is based on a special machine learning architecture that can model data collections which are intrinsically hierarchical. It…

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MetaCV
Desktop

MetaCV Metagenome Composition Vector

A composition and phylogeny-based algorithm to classify very short metagenomic…

A composition and phylogeny-based algorithm to classify very short metagenomic reads (75-100 bp) into specific taxonomic and functional groups. MetaCV performs (for both sensitivity and specificity)…

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CoMeta
Desktop

CoMeta Classification of Metagenomes

A tool used to assign a query read (a DNA fragment) from metagenomic sample…

A tool used to assign a query read (a DNA fragment) from metagenomic sample into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus),…

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lattice-metage
Desktop

lattice-metage

Allows clustering of metagenomic datasets. lattice-metage is a two-dimensional…

Allows clustering of metagenomic datasets. lattice-metage is a two-dimensional lattice model that can incorporate information from multiple models. The software backs-off to a combination of multiple…

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sourmash
Desktop

sourmash

Allows users to create, compare, and manipulate MinHash sketches of genomic…

Allows users to create, compare, and manipulate MinHash sketches of genomic data. sourmash consists in a library for MinHash sketches, which enables identification of samples and data sets with…

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Bracken
Desktop

Bracken Bayesian Reestimation of Abundance after Classification with KrakEN

A highly accurate statistical method that computes the abundance of species in…

A highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Bracken uses the taxonomy labels assigned by Kraken, a highly accurate…

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MetaPalette
Desktop

MetaPalette

A k-mer based bacterial community reconstruction technique that utilizes…

A k-mer based bacterial community reconstruction technique that utilizes sparsity promoting ideas from the field of compressed sensing to reconstruct the composition of a bacterial community. This…

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MetaFlow
Desktop

MetaFlow

A method based on coverage analysis across entire genomes that also scales to…

A method based on coverage analysis across entire genomes that also scales to high-throughput sequencing (HTS) samples. We formulated this problem as an NP-hard matching problem in a bipartite graph,…

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Sequedex
Desktop

Sequedex

A signature-based method to classify the function and phylogeny of reads as…

A signature-based method to classify the function and phylogeny of reads as short as 30 bp.

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RITA
Desktop
Web

RITA Rapid Identification of Taxonomic Assignments

Uses the agreement between composition and homology to accurately classify…

Uses the agreement between composition and homology to accurately classify sequences as short as 50 nt in length by assigning them to different classification groups with varying degrees of…

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RIEMS
Desktop

RIEMS Reliable Information Extraction from Metagenomic Sequence datasets

Assigns every individual read sequence within a dataset taxonomically by…

Assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After…

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FOCUS
Desktop
Web

FOCUS

A sensitive and fast solution to bin metagenomic samples. FOCUS2 first runs…

A sensitive and fast solution to bin metagenomic samples. FOCUS2 first runs FOCUS to predict the taxa in the sample taxa and refines the profiling using a fast aligner with a reduced version of the…

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CensuScope
Desktop

CensuScope Census-based rapid and accurate metagenome taxonomic profiling.

A rapid and accurate metagenome taxonomic profiling tool that randomly extracts…

A rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. CensuScope allows assessment of…

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Binpairs
Desktop

Binpairs

Simple but effective strategies of utilizing pairing-information of Illumina…

Simple but effective strategies of utilizing pairing-information of Illumina short reads. The proposed strategies have been compiled together as a user-friendly tool named 'Binpairs', which…

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WGSQuikr
Desktop

WGSQuikr

A reconstruction method that can compute a vector of taxonomic assignments and…

A reconstruction method that can compute a vector of taxonomic assignments and their proportions in the sample with remarkable speed and accuracy. WGSQuikr represents a new class of metagenomics…

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HTTMM
Desktop

HTTMM Hierarchical Taxonomy Tree-based Mixture Model

Estimates the abundance of taxon within a microbial community by incorporating…

Estimates the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome specific short reads and homologous short reads among genomes…

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One Codex
Web

One Codex

Identifies microbial sequences using a "k-mer based" taxonomic…

Identifies microbial sequences using a "k-mer based" taxonomic classification algorithm through a web-based data platform, using a reference database that currently includes approximately…

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MTR
Desktop

MTR Multiple Taxonomic Ranks

Exploits information shared by reads. MTR is a method for tackling drawbacks…

Exploits information shared by reads. MTR is a method for tackling drawbacks using clustering at Multiple Taxonomic Ranks. Specifically, MTR consists of two main phases. First, for each taxonomic…

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SPANNER
Desktop

SPANNER Simularity Profile ANNotatER

Extends LCA to perform supervised homology-based taxonomic classification of…

Extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.

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TAEC
Desktop

TAEC Taxonomic Analysis by Elimination and Correction

A homology-based approach that utilizes the similarity in the genomic sequence…

A homology-based approach that utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. By taking account of the similarity in the genomic sequence TAEC…

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PhyloSift
Desktop

PhyloSift

A method for phylogenetic analysis of metagenomic samples and for comparison of…

A method for phylogenetic analysis of metagenomic samples and for comparison of community structure among multiple related samples. PhyloSift leverages phylogenetic models of molecular evolution to…

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INDUS
Web

INDUS

A composition-based approach that incorporates the following novel features.…

A composition-based approach that incorporates the following novel features. First, INDUS discards the 'one genome-one composition' model adopted by existing compositional approaches.…

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MetaBinG
Desktop

MetaBinG

An ultra-fast metagenomic sequence classification system using graphic…

An ultra-fast metagenomic sequence classification system using graphic processing units (GPUs). The accuracy of MetaBinG is comparable to the best existing systems and it can classify a million of…

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TAMER
Desktop

TAMER

An R package for accurate taxonomic assignment of metagenomic sequencing reads.…

An R package for accurate taxonomic assignment of metagenomic sequencing reads. The proposed method was comprehensively tested on both simulated datasets and two real datasets. TAMER assigns reads to…

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ORION-VIRCAT
Dataset

ORION-VIRCAT

Serves as a resource for the integration and verification of taxonomical…

Serves as a resource for the integration and verification of taxonomical classifications generated by the International Committee on the Taxonomy of Viruses (ICTV) and the National Center for…

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NBC
Web

NBC Naïve Bayes Classification

The Naïve Bayes Classification tool webserver for taxonomic classification of…

The Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads.

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TWARIT
Web

TWARIT

A hybrid approach designed to achieve extremely rapid phylogenetic…

A hybrid approach designed to achieve extremely rapid phylogenetic classification of metagenomic sequences. TWARIT makes use of both 'sequence similarity' and 'sequence…

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Taxo_pack
Desktop

Taxo_pack

Allows analysis and visualization of the taxonomic abundance of set of…

Allows analysis and visualization of the taxonomic abundance of set of sequences.

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CrossClassify
Desktop

CrossClassify

Permits to map results of metagenomic analyses from one taxonomy onto another.…

Permits to map results of metagenomic analyses from one taxonomy onto another. CrossClassify contains the five taxonomies following: SILVA, RDP, Greengenes, NCBI, and OTT. It allows the user to…

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MetaBin
Desktop
Web

MetaBin

Serves to realize the taxonomic analysis. MetaBin works as a desktop program…

Serves to realize the taxonomic analysis. MetaBin works as a desktop program and a web server. The web server can serve to do analysis by either submitting reads or Blastx output. Program and web…

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taxgetrank
Desktop

taxgetrank

Gets parents of taxon(s). taxgetrank reads in one or more taxons, and reports…

Gets parents of taxon(s). taxgetrank reads in one or more taxons, and reports the taxons at each level from the current to the top. The taxon input may be a literal sequence or read from a database,…

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TAC-ELM
Desktop

TAC-ELM Taxonomic Classification with Extreme Learning Machines

A sequence composition-based taxonomic classifier using extreme learning…

A sequence composition-based taxonomic classifier using extreme learning machines referred to as TAC-ELM for metagenomic analysis. TAC-ELM uses the framework of extreme learning machines to quickly…

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PhyloPythia
Web

PhyloPythia

Phylogenetically classifies variable-length DNA sequence fragments. PhyloPythia…

Phylogenetically classifies variable-length DNA sequence fragments. PhyloPythia is a method that uses sequence composition to phylogenetically characterize sequence fragments. The software allows the…

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SOrt-ITEMS
Desktop
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SPHINX
Desktop

SPHINX

A hybrid binning approach that achieves high binning efficiency by utilizing…

A hybrid binning approach that achieves high binning efficiency by utilizing both 'compositional' and 'similarity' features of the query sequence during the binning process.

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DiScRIBinATE
Desktop

DiScRIBinATE Distance Score Ratio for Improved Binning And Taxonomic Estimation

Allows taxonomic classification of metagenomic sequences. DiScRIBinATE attempts…

Allows taxonomic classification of metagenomic sequences. DiScRIBinATE attempts to address the limitations associated with the software SOrt-ITEMS. To maintain the accuracy of assignments, the…

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ProViDE
Desktop

ProViDE Program for Viral Diversity Estimation

A novel similarity based binning algorithm that uses a customized set of…

A novel similarity based binning algorithm that uses a customized set of alignment parameter thresholds/ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences.

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XplorSeq
Desktop

XplorSeq

Facilitates the compilation, management and phylogenetic analysis of DNA…

Facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences.…

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GSTaxClassifier
Web

GSTaxClassifier Genomic Signature based Taxonomic Classifier

A program for metagenomics analysis of shotgun DNA sequences. GSTaxClassifier…

A program for metagenomics analysis of shotgun DNA sequences. GSTaxClassifier includes a simple but effective algorithm, a modification of the Bayesian method, to predict the most probable genomic…

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