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Bacteria taxonomy detection software tools | Genome annotation

Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic…
Strain Solution
Desktop

Strain Solution

Serves for a routine diagnostic use in microbial laboratories. Strain Solution…

Serves for a routine diagnostic use in microbial laboratories. Strain Solution is a program that characterize the mixtures of closely related bacteria by using their own biomarker peaks specific to…

LPSN
Dataset

LPSN List of Prokaryotic Names with Standing in Nomenclature

Gathers the names of prokaryotes (Bacteria and Archaea) published in the…

Gathers the names of prokaryotes (Bacteria and Archaea) published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) directly or by inclusion in a Validation List, under…

NCBI Taxonomy…
Dataset

NCBI Taxonomy Database

Supplies solution to annotate sequences. The NCBI Taxonomy Database serves as…

Supplies solution to annotate sequences. The NCBI Taxonomy Database serves as the standard nomenclature and classification for the International Sequence Database (INSD). This database provides tools…

Metacoder
Desktop

Metacoder

Allows the user to easily manipulate, parse and visualize metabarcoding data…

Allows the user to easily manipulate, parse and visualize metabarcoding data for microbial taxonomy identification. Many used formats are supported, containing sequences, taxons or classification.…

SeqSero
Web
Desktop

SeqSero

Allows identification of Salmonella serotypes that use high-throughput genome…

Allows identification of Salmonella serotypes that use high-throughput genome sequencing data. SeqSero contains functions permitting determination from genome assemblies or raw sequencing reads. This…

LOCUST
Desktop
Web

LOCUST LOcus CUstom Sequence Typer

Allows users to customize the typing of microbial isolates from whole genome…

Allows users to customize the typing of microbial isolates from whole genome sequencing (WGS) data. LOCUST can generate a seed file from a given set of alleles. It is able to type bacterial genomes…

FurIOS
Web

FurIOS

Identifies bacteria from the Vibrionaceae family thank to their fur-sequence.…

Identifies bacteria from the Vibrionaceae family thank to their fur-sequence. FurIOS was tested on the classification of environmental Vibrionaceae strains belonging to the global culture collection…

MetaTopics
Desktop

MetaTopics

Allows to extract the latent microbial communities which reflects the intrinsic…

Allows to extract the latent microbial communities which reflects the intrinsic relations or interactions among several major microbes. MetaTopics is based on state-of-arts topic model derived from…

MicroTaxi
Web
Desktop

MicroTaxi Microbial Taxonomic Identification

A comprehensive method which uses the taxon-specific genes for the correct…

A comprehensive method which uses the taxon-specific genes for the correct taxonomic assignment of existing and new bacterial genomes. MicroTaxi provides an alternate valuable methodology to carry…

SISTR
Web
Desktop

SISTR Salmonella In Silico Typing Resource

A bioinformatics platform for rapidly performing simultaneous in silico…

A bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar…

CETAF Stable…
Web

CETAF Stable Identifiers

Follows Linked Open Data principles and implements redirection mechanisms to…

Follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing…

KmerFinderJS
Desktop
Web

KmerFinderJS

Predicts prokaryotic species based on the number of overlapping (co-occurring)…

Predicts prokaryotic species based on the number of overlapping (co-occurring) k-mers between the query genome and genomes in a reference database. KmerFinderJS, an implementation of KmerFinder, is a…

BioMaS
Web

BioMaS Bioinformatic analysis of Metagenomic AmpliconS

A bioinformatic pipeline designed to support biomolecular researchers involved…

A bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities. BioMaS uses completely automated workflow, comprehensive of…

Reads2Type
Web

Reads2Type

A web-based tool for taxonomy identification based on whole bacterial genome…

A web-based tool for taxonomy identification based on whole bacterial genome sequence data. In comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing…

rMLST
Web

rMLST ribosomal MultiLocus Sequence Typing

An approach that indexes variation of the 53 genes encoding the bacterial…

An approach that indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes) as a means of integrating microbial taxonomy and typing. The rps gene variation…

TaxonomyFinder
Web

TaxonomyFinder

Performs predictions for draft or complete genomes but not for short reads.…

Performs predictions for draft or complete genomes but not for short reads. TaxonomyFinder is based on species-specific functional protein domain profiles. The workflow of this method is a four-step…

taxget
Desktop

taxget

Gets one or more taxons. taxget reads one or more taxons and writes them out…

Gets one or more taxons. taxget reads one or more taxons and writes them out again. The taxon input may be a literal sequence or read from a database, file, file of taxon names, or even the…

taxgetup
Desktop

taxgetup

Gets parents of one or more taxons. taxgetup accepts as input a literal…

Gets parents of one or more taxons. taxgetup accepts as input a literal sequence or read from a database, file, file of taxon names, or even the command-line or the output of another programs. The…

SpeciesFinder
Web

SpeciesFinder

Predicts the prokaryotic species based on the 16S rRNA gene. SpeciesFinder is…

Predicts the prokaryotic species based on the 16S rRNA gene. SpeciesFinder is an online method based on the 16S rRNA gene, which has served as the backbone of prokaryotic systematics since 1977. It…

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