A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species. Due to the extensive within-species diversity in the microbial world, the pan-genome is often many times larger than a single genome. Studies of pan-genomes have…
Integrated Toolkit… Integrated Toolkit for Exploration of microbial…

ITEP Integrated Toolkit for Exploration of microbial Pan-genomes

A suite of scripts and Python libraries for the comparison of microbial…

A suite of scripts and Python libraries for the comparison of microbial genomes. ITEP includes tools for de novo protein family prediction by clustering, ortholog detection, analysis of functional…

Desktop app
Bacterial Pan Genome… Bacterial Pan Genome Analysis pipeline

BPGA Bacterial Pan Genome Analysis pipeline

A perl based pipeline to exploit protein clustering data for complete…

A perl based pipeline to exploit protein clustering data for complete pan-genome analysis of bacterial species. In addition to all types of routine pan-genomic analyses, BPGA includes a number of…

Web app
Phandango Phandango

Phandango

Allows visualisation of a phylogenetic tree, associated metadata and genomic…

Allows visualisation of a phylogenetic tree, associated metadata and genomic information such as recombination blocks, pan-genome contents or GWAS results. Phandango is an interactive web app…

Desktop app
G T A T C G C T A De-Novo Genome… De-Novo Genome Analysis Pipeline

DeNoGAP De-Novo Genome Analysis Pipeline

Performs reference-assisted and de novo gene prediction, homolog protein family…

Performs reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis. DeNoGAP integrates bioinformatics…

Rice PAN-genome… Rice PAN-genome Browser

RPAN Rice PAN-genome Browser

A comprehensive dataset of rice sequences. RPAN presents analysis results from…

A comprehensive dataset of rice sequences. RPAN presents analysis results from 3K rice genome data which provides new perspective for rice researchers and breeding experts. RPAN includes the…

Web app
Desktop app
GView GView

GView

An application for viewing and examining prokaryotic genomes in a circular or…

An application for viewing and examining prokaryotic genomes in a circular or linear context. GView accepts standard sequence file formats and an optional style specification file to generate…

panX panX

panX

Breaks the annotated genomes of a large number of strain into genes and further…

Breaks the annotated genomes of a large number of strain into genes and further clusters annotated genes into orthologous groups. panX is a web-based environment for microbial pan-genome data…

Desktop app
PanViz PanViz

PanViz

Permits visualization of pangenome analysis. PanViz allows visualization of…

Permits visualization of pangenome analysis. PanViz allows visualization of changes in gene group classification as different subsets of pangenomes are selected, as well as comparisons of individual…

Desktop app
Pan-Tetris Pan-Tetris

Pan-Tetris

An interactive software tool that provides a clearly structured and suitable…

An interactive software tool that provides a clearly structured and suitable way for the visual inspection of gene occurrences in a pan-genome table. Pan-Tetris allows the user to modify the…

Desktop app
PanTools PanTools

PanTools

An implementation of a pan-genome representation based on the Neo4j graph…

An implementation of a pan-genome representation based on the Neo4j graph database, focusing on the application to large sets of complex eukaryotic genomes. PanTools allows for the construction of…

Desktop app
Bloom Filter Trie Bloom Filter Trie

BFT Bloom Filter Trie

An alignment-free, reference-free and incremental data structure for storing a…

An alignment-free, reference-free and incremental data structure for storing a pan-genome as a colored de Bruijn graph. The data structure allows to store and compress a set of colored k-mers, and…

Desktop app
compressed deBruijn… compressed deBruijn Graph

compressed deBruijn Graph

Two space-efficient methods to build the compressed de Bruijn graph from…

Two space-efficient methods to build the compressed de Bruijn graph from scratch. An experimental comparison with splitMEM showed that our algorithms are more than an order of magnitude faster than…

Desktop app
SplitMEM SplitMEM

SplitMEM

Computes a graphical representation of the pan-genome by exploiting the deep…

Computes a graphical representation of the pan-genome by exploiting the deep relationships between suffix trees and compressed de Bruijn graphs. Maximal exact matches (MEMs) are readily identified in…

Desktop app
Pangenome-based… Pangenome-based Functional Profiles

PanFP Pangenome-based Functional Profiles

Infers functional profiles of microbial communities from 16S rRNA gene survey…

Infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit…

Desktop app
Large-Scale BLAST… Large-Scale BLAST Score Ratio

LS-BSR Large-Scale BLAST Score Ratio

Rapidly compares the genetic content of hundreds to thousands of bacterial…

Rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This…

Desktop app
Pan-genome Ortholog… Pan-genome Ortholog Clustering Tool

PanOCT Pan-genome Ortholog Clustering Tool

A tool for pan-genomic analysis of closely related prokaryotic species or…

A tool for pan-genomic analysis of closely related prokaryotic species or strains. PanOCT uses conserved gene neighborhood information to separate recently diverged paralogs into orthologous clusters…

Desktop app
Roary Roary

Roary

A tool that rapidly builds large-scale pan genomes, identifying the core and…

A tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard…

Desktop app
Web app
AGEnt AGEnt

AGEnt

Performs in silico subtractive hybridization of core genome sequences, such as…

Performs in silico subtractive hybridization of core genome sequences, such as those produced by Spine, against a query genomic sequence to identify accessory genomic sequences (AGEs) in the query…

Desktop app
PanCake PanCake

PanCake

Provides analysis of pangenomes, namely the identification of genomic regions…

Provides analysis of pangenomes, namely the identification of genomic regions present in all strains of a given genome set (i.e. the core genome), or the identification of regions unique to a single…

Web app
PANNOTATOR PANNOTATOR

PANNOTATOR

A web-based automated pipeline for the annotation of closely related and…

A web-based automated pipeline for the annotation of closely related and well-suited genomes for pan-genome studies, aiming at reducing the manual work to generate reports and corrections of various…

Desktop app
Web app
Spine Spine

Spine

Identifies a core genome from input genomic sequences. Sequences are aligned…

Identifies a core genome from input genomic sequences. Sequences are aligned using Nucmer and regions found to be in common between all or a user-defined subset of genomes will be returned. Sequences…

Desktop app
eCAMBer eCAMBer

eCAMBer

A tool for efficiently supporting comparative analysis of multiple bacterial…

A tool for efficiently supporting comparative analysis of multiple bacterial strains within the same species. eCAMBer is a highly optimized revision of CAMBer, scaling it up for significantly larger…

Web app
PanCGHweb PanCGHweb

PanCGHweb

Pangenome microarrays allow determining the genomic content of bacterial…

Pangenome microarrays allow determining the genomic content of bacterial strains more accurately than conventional comparative genome hybridization microarrays. PanCGHweb is a tool that effectively…

Web app
PanGP PanGP

PanGP

A tool for quickly analyzing bacterial pan-genome profile. It has integrated…

A tool for quickly analyzing bacterial pan-genome profile. It has integrated two kinds of sample algorithm, so that it could calculate the pan-genome profile of a population with dozens of or…

Desktop app
Web app
Panseq Panseq

Panseq

Determines the core and accessory regions among a collection of genomic…

Determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. Panseq readily extracts regions unique to a genome or group of genomes, identifies…

Web app
Prokaryotic Genome… Prokaryotic Genome Analysis Tool

PGAT Prokaryotic Genome Analysis Tool

A web-based database tool originally developed as a platform by which to…

A web-based database tool originally developed as a platform by which to provide rapid analysis of bacterial genomes sequenced using next generation technologies. Multi-strain comparison of microbial…

Desktop app
micropan micropan

micropan

An R package for the study of prokaryotic pan-genomes. The R computing…

An R package for the study of prokaryotic pan-genomes. The R computing environment harbors endless possibilities with respect to statistical analyses and graphics. External free software is used for…

Desktop app
Pan-Genome Analysis… Pan-Genome Analysis Pipeline

PGAP Pan-Genome Analysis Pipeline

Performs five analytic functions with only one command, including cluster…

Performs five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution…

Desktop app
Harvest Harvest

Harvest

A suite of core-genome alignment and visualization tools for quickly analyzing…

A suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a…

Desktop app
GET_HOMOLOGUES GET_HOMOLOGUES

GET_HOMOLOGUES

An open-source software package that builds on popular orthology-calling…

An open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians.…

Web app
BLASTatlas Deprecated BLASTatlas

BLASTatlas

A visualization method that allows easy comparison of many sequenced genomes to…

A visualization method that allows easy comparison of many sequenced genomes to a defined reference strain. The BLASTatlas is useful for mapping and visualizing whole genome homology of genes and…

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