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Whole genome alignment software tools | Comparative genomics

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…
POGO-DB
Dataset

POGO-DB

Allows users to compare, visualize and summarize genome and marker genes.…

Allows users to compare, visualize and summarize genome and marker genes. POGO-DB contains a graphical interface on which it is possible to visualize the information. This database provides user a…

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LAST-TRAIN
Desktop
Web

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…

kSNP
Desktop

kSNP

Allows identification and phylogenetic analysis without requiring genome…

Allows identification and phylogenetic analysis without requiring genome alignment or the reference genomes. kSNP annotates single nucleotide polymorphisms (SNPs) by automatically downloading the the…

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SPANDx
Desktop

SPANDx Synergised Pipeline for Analysis of NGS Data in Linux

Consolidates several well-validated, open-source packages into a single tool,…

Consolidates several well-validated, open-source packages into a single tool, mitigating the need to learn and manipulate individual next-generation sequencing (NGS) programs. SPANDx is an all-in-one…

ANItools
Web
Desktop

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…

MUMmer
Desktop

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…

META-GECKO
Desktop

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…

chainCleaner
Desktop

chainCleaner

Improves the specificity in genome alignments by accurately detecting and…

Improves the specificity in genome alignments by accurately detecting and removing local alignments that obscure the evolutionary history of genomic rearrangements. chainCleaner improves the…

Alpha
Desktop

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…

BADGE
Desktop

BADGE BlAst Diagnostic Gene findEr

Predicts diagnostic marker genes (DMGs) for a strain specific trait, starting…

Predicts diagnostic marker genes (DMGs) for a strain specific trait, starting with phenotyping up to the point of validation using polymerase chain reaction (PCR). BADGE is a free tool, which, in…

LAST
Web
Desktop

LAST

Enables fast and sensitive comparison of large sequences with arbitrarily…

Enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition. LAST can handle big sequence data, e.g: compare two vertebrate genomes and align billions of DNA…

LASTM
Desktop

LASTM

Allows to improve the sensitivity of existing whole-genome alignment software.…

Allows to improve the sensitivity of existing whole-genome alignment software. LASTM is based on LAST and uses in addition the "seed-and-extend" heuristic method. It avoids introducing…

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lncRNA-screen
Desktop

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…

Alignathon
Dataset

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…

Harvest
Desktop

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…

BRANE Clust
Desktop

BRANE Clust

Refines gene regulatory network (GRN) inference thanks to cluster information.…

Refines gene regulatory network (GRN) inference thanks to cluster information. BRANE Clust works as a post-processing tool for inference methods. The clustering is based on the inversion of a system…

rNA
Desktop

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…

Multi-LAGAN
Web

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.

Gegenees
Desktop

Gegenees

Compares genome sequences (Draft and Completed). Gegenees was primarily…

Compares genome sequences (Draft and Completed). Gegenees was primarily developed for bacterial genomes but it is also possible to use on viruses and smaller eukaryotes. Gegenees fragments the…

GECKO-MGV
Web

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…

GW-CALL
Desktop

GW-CALL Genome-Wide variant CALLer

Calls variants within the genome based on all mappable reads. GW-CALL exploits…

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 into several…

GenomeVISTA
Desktop
Web

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…

GECKO
Desktop

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…

YOC
Desktop

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…

MiModD
Desktop

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…

REVEAL
Desktop

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…

MGA
Desktop

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…

MAGIC
Desktop

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…

progressiveMauv…
Desktop

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…

M-GCAT
Desktop

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…

IDBA-hybrid
Desktop

IDBA-hybrid Iterative De Bruijn graph de novo Assembler-hybrid for hybrid sequencing

Allows users to de novo assemble hybrid sequences. IDBA-hybrid assists de novo…

Allows users to de novo assemble hybrid sequences. IDBA-hybrid assists de novo assembly by using a closed related reference genome. It makes alignments between reads and reference first to extract…

GAME
Desktop

GAME Genome Alignment by Match Extension

Provides a pairwise local alignment program for genomic DNA sequences based on…

Provides a pairwise local alignment program for genomic DNA sequences based on maximal exact match (MEM) anchor. GAME is a fast and accurate anchor filtering scheme based on simple match extension.…

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