The huge number of genomes sequenced every day makes the development of effective comparison and alignment tools ever more urgent. Indeed, many microbiological applications rely directly on genome alignments, for instance micro-diversity and phylogenomic analysis of bacterial…
Desktop app
MUMmer MUMmer

MUMmer

Compares eukaryotic genomes at varying evolutionary distances. MUMmer is a…

Compares eukaryotic genomes at varying evolutionary distances. MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. MUMmer can also align incomplete genomes; it…

Web app
Multi Genome Viewer Multi Genome Viewer

GECKO-MGV Multi Genome Viewer

A web app to display, browse and analyse the results of genome comparison…

A web app to display, browse and analyse the results of genome comparison produced by GECKO and GECKO-CSB. This tool is composed of several independent modules that execute specific tasks for the…

Desktop app
META-GECKO META-GECKO

META-GECKO

A set of post-processing tools aimed at improving the taxonomical…

A set of post-processing tools aimed at improving the taxonomical classification and at providing additional information to enhance metagenomics analyses. The developed tools provide additional…

Desktop app
MiModD MiModD

MiModD

Developed for the identification and annotation of mutations in the genomes of…

Developed for the identification and annotation of mutations in the genomes of model organisms from whole-genome sequencing data. MiModD was designed specifically to enable biologists/geneticists…

Web app
Desktop app
ANItools ANItools

ANItools

A web app for defining the relationship between bacterial strains and…

A web app for defining the relationship between bacterial strains and contributing to the classification and identification of bacterial species using genome data. ANItools helps users directly get…

Desktop app
ALignment of PHAges ALignment of PHAges

Alpha ALignment of PHAges

A mathematical model based on partial order graphs for performing multiple…

A mathematical model based on partial order graphs for performing multiple alignment of bacteriophage whole genomes, along with algorithms to operate on the model. Relying exclusively on the equality…

Desktop app
GEnome Comparison… GEnome Comparison with K-mers Out-of-core

GECKO GEnome Comparison with K-mers Out-of-core

A package to identify collections of high-scoring segment pairs by pairwise…

A package to identify collections of high-scoring segment pairs by pairwise genome comparison procedures, that can then be used to obtain gapped fragments. GECKO facilitates massive comparisons of…

Desktop app
Web app
G T A T C G C T A LAST-TRAIN LAST-TRAIN

LAST-TRAIN

Improves sequence alignment accuracy by inferring substitution and gap scores…

Improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. LAST-TRAIN uses a standard…

Desktop app
randomized Numerical… randomized Numerical Aligner

rNA randomized Numerical Aligner

Supports the alignment of single and paired-end reads, and it can run on both…

Supports the alignment of single and paired-end reads, and it can run on both parallel and distributed architectures. rNA is divided into two distinct computational steps: reference genome…

Desktop app
A A A lncRNA-screen lncRNA-screen

lncRNA-screen

A comprehensive pipeline for computationally screening putative long non-coding…

A comprehensive pipeline for computationally screening putative long non-coding RNA (lncRNA) transcripts over large multimodal datasets. lncRNA-screen main objective is to facilitate the…

Desktop app
Genome-Wide variant… Genome-Wide variant CALLer

GW-CALL Genome-Wide variant CALLer

A package to calls variants within the genome based on all mappable reads.…

A package to calls variants within the genome based on all mappable reads. GW-CALL exploits information of all reads in a genome-wide decision making process : in particular, it partitions the genome…

Desktop app
REcursiVe… REcursiVe Exact-matching ALigner

REVEAL REcursiVe Exact-matching ALigner

A ‘recursive exact matching’ approach that is capable of aligning…

A ‘recursive exact matching’ approach that is capable of aligning whole-genomes. REVEAL can be used to detect various structural variations from two de-novo human genome assemblies. REVEAL can…

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
kSNP kSNP

kSNP

A program for SNP identification and phylogenetic analysis without genome…

A program for SNP identification and phylogenetic analysis without genome alignment or the requirement for reference genomes. The kSNP3.0 package also includes a number of new tools and utilities…

Desktop app
M-GCAT M-GCAT

M-GCAT

A tool for rapidly visualizing and aligning the most highly conserved regions…

A tool for rapidly visualizing and aligning the most highly conserved regions in multiple (typically prokaryote) genomes. M-GCAT is based upon a highly efficient approach to anchor-based multiple…

Web app
Multi-LAGAN Multi-LAGAN

Multi-LAGAN

A system for multiple global alignment of genomic sequences. Multi-LAGAN is a…

A system for multiple global alignment of genomic sequences. Multi-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evolutionary distance.

Desktop app
Web app
GenomeVISTA GenomeVISTA

GenomeVISTA

Unifies in one package multiple capabilities necessary to carry out various…

Unifies in one package multiple capabilities necessary to carry out various types of comparative analysis of genomic sequences and whole-genome assemblies. GenomeVISTA aligns sequences both in…

Desktop app
Multiple Genome… Multiple Genome Aligner

MGA Multiple Genome Aligner

A software tool that efficiently computes multiple genome alignments of large,…

A software tool that efficiently computes multiple genome alignments of large, closely related DNA sequences. For example, MGA can align 85% percent of the complete genomes of six human adenoviruses…

Desktop app
MAGIC MAGIC

MAGIC

An integrative and accurate method for comparative genome mapping. MAGIC…

An integrative and accurate method for comparative genome mapping. MAGIC consists of two phases: preprocessing for identifying "maximal similar segments," and mapping for clustering and…

Desktop app
progressiveMauve progressiveMauve

progressiveMauve

A platform for comparative genomic and population genomic studies. Key features…

A platform for comparative genomic and population genomic studies. Key features of the approach are an anchor scoring function that penalizes alignment anchoring in repetitive regions of the genome…

Desktop app
YOC YOC

YOC

A whole genome alignment tool designed for collinear genomes. YOC has several…

A whole genome alignment tool designed for collinear genomes. YOC has several advantages over existing genome aligners: (1) it is based on a simplified two phase alignment strategy, (2) it is easy to…

Alignathon Alignathon

Alignathon

A collaborative competition to assess the state of the art in whole genome…

A collaborative competition to assess the state of the art in whole genome sequence alignment. The Alignathon is a collaborative project to assess whole genome aligners and promote development of the…

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