The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in…
SyntenyTracker
Web

SyntenyTracker

An automated tool for the identification of homologous synteny blocks (HSBs)…

An automated tool for the identification of homologous synteny blocks (HSBs) between genomes that tolerates errors common in radiation-hybrid (RH) comparative maps and can be used for automated…

MCScan
Desktop

MCScan Multiple Collinearity Scan

Scans multiple genomes or subgenomes in order to identify putative homologous…

Scans multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and aligns these regions using genes as anchors. MCscan takes the predicted pairwise segments from…

AutoGRAPH
Web

AutoGRAPH

An interactive web server for automatic multi-species comparative genomics…

An interactive web server for automatic multi-species comparative genomics analyses based on personal datasets or pre-inserted public datasets. AutoGRAPH automatically identifies conserved segments…

Sibelia
Desktop

Sibelia Synteny Block ExpLoration tool

Assists biologists in analysing the genomic variations that correlate with…

Assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for…

MCScanX
Desktop

MCScanX

A toolkit that implements an adjusted MCScan algorithm for detection of synteny…

A toolkit that implements an adjusted MCScan algorithm for detection of synteny and collinearity and incorporates 14 computer programs for visualizing and analyzing identified synteny and…

SyMAP
Desktop

SyMAP Synteny Mapping and Analysis Program

A software package for detecting, displaying, and querying syntenic…

A software package for detecting, displaying, and querying syntenic relationships between sequenced chromosomes and/or fingerprint contig physical maps. SyMAP uses MUMmer to compute the raw hits…

SynFind
Web
Desktop

SynFind

Identifies all syntenic regions to a given gene in a user-selected set of…

Identifies all syntenic regions to a given gene in a user-selected set of genomes, regardless of whether the gene is still present in that region. SynFind is powered by an algorithm that calculates…

SimpleSynteny
Web
Desktop

SimpleSynteny

A web-based platform capable of directly interrogating collinearity of local…

A web-based platform capable of directly interrogating collinearity of local genomic neighbors across multiple species in a targeted manner. SimpleSynteny provides a pipeline for evaluating the…

Synteny Portal
Web

Synteny Portal

A versatile web-based application portal that allows for construction,…

A versatile web-based application portal that allows for construction, visualization and browsing of synteny blocks by compensating limitations of existing tools. With Synteny Portal, users can…

Cyntenator
Desktop

Cyntenator

A flexible and scalable tool for the identification of conserved gene orders…

A flexible and scalable tool for the identification of conserved gene orders across multiple species over long evolutionary distances. CYNTENATOR does not depend on nucleotide-level alignments and a…

Mugsy
Desktop

Mugsy

A multiple alignment tool for whole genomes. Mugsy uses Nucmer for pairwise…

A multiple alignment tool for whole genomes. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive…

QUOTA-ALIGN
Desktop

QUOTA-ALIGN

Screens a set of synteny blocks to retain only those compatible with a user…

Screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. QUOTA-ALIGN can be used to solves the problem of selecting a subset of…

Aequatus
Desktop

Aequatus

A standalone web-based tool that provides an in-depth view of gene structure…

A standalone web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations. Aequatus relies on pre-calculated…

PhylDiag
Desktop

PhylDiag

Identifies statistically significant synteny blocks in pairwise comparisons of…

Identifies statistically significant synteny blocks in pairwise comparisons of eukaryote genomes. Compared to previous methods, PhylDiag uses gene trees to define gene homologies, thus allowing gene…

ColinearScan
Desktop

ColinearScan

A statistical approach to detect homologous chromosomal segments based on gene…

A statistical approach to detect homologous chromosomal segments based on gene colinearity. We implement this approach in a software package ColinearScan to detect putative colinear regions using a…

mGSV
Web

mGSV multi-Genome Synteny Viewer

A web-based synteny visualization tool that enhances the original…

A web-based synteny visualization tool that enhances the original functionalities of GSV by allowing biologists to upload their own datasets and visualize the synteny among multiple genomes…

Synorth
Data

Synorth SYNteny and ORTholog

A web resource for exploring and categorizing the syntenic relationships in…

A web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication…

DAGchainer
Desktop

DAGchainer

Computes chains of syntenic genes found within complete genome sequences. Given…

Computes chains of syntenic genes found within complete genome sequences. Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between…

FISH
Desktop

FISH Fast Identification of Segmental Homology

A flexible dynamic programming algorithm for the identification of segments…

A flexible dynamic programming algorithm for the identification of segments having multiple homologous features. We model the probability of observing putative segmental homologies by chance and…

OrthoCluster
Web
Desktop

OrthoCluster

A fast and easy-to-use program for the identification of synteny blocks among…

A fast and easy-to-use program for the identification of synteny blocks among multiple genomes. OrthoCluster allows users to identify synteny blocks that contain different types of mismatches, and to…

SynChro
Desktop

SynChro

A fast, efficient and user-friendly tool to reconstruct synteny blocks between…

A fast, efficient and user-friendly tool to reconstruct synteny blocks between (complex) genomes harboring different levels of synteny conservation. Its main properties are the followings: (i) it…

OSfinder
Desktop

OSfinder Orthologous Segment finder

Uses a novel scoring scheme based on stochastic models. OSfinder takes as input…

Uses a novel scoring scheme based on stochastic models. OSfinder takes as input the positions of short homologous regions (also referred to as anchors) and explicitly discriminates orthologous…

Murasaki
Desktop

Murasaki

Provides an open source platform to take advantage of long patterns, cluster…

Provides an open source platform to take advantage of long patterns, cluster computing, and novel hash algorithms to produce accurate anchors across multiple genomes with computational efficiency…

Proteny
Desktop

Proteny

Detects synteny between diverged genomes. Proteny operates on the amino acid…

Detects synteny between diverged genomes. Proteny operates on the amino acid sequence level to be insensitive to codon usage adaptations and clusters groups of exons disregarding order to handle…

i-ADHoRe
Desktop

i-ADHoRe iterative Automatic Detection of Homologous Regions

Combines gene content and gene order information of homologous genomic segments…

Combines gene content and gene order information of homologous genomic segments into profiles to detect highly degenerated homology relations within and between genomes. Unlike other tools, i-ADHoRe…

DRIMM-Synteny
Desktop

DRIMM-Synteny Duplications and Rearrangements In Multiple Mammals-Synteny

Most synteny block reconstruction algorithms use genes shared over all genomes…

Most synteny block reconstruction algorithms use genes shared over all genomes to construct the synteny blocks for multiple genomes. However, the number of genes shared among all genomes quickly…

G T A T C G C T A
r2cat
Desktop

r2cat related reference contig arrangement tool

It is able to quickly match a set of contigs onto a related genome, order the…

It is able to quickly match a set of contigs onto a related genome, order the contigs according to their matches and display the result in an interactive synteny plot. The matching, however, is not…

Cinteny
Web

Cinteny

Compares multiple genomes and performs sensitivity analysis for synteny block…

Compares multiple genomes and performs sensitivity analysis for synteny block detection and for the subsequent computation of reversal distances. Cinteny can also be used to interactively browse…

MCMuSeC
Desktop

MCMuSeC Max-gap Clusters by Multiple Sequence Comparison

Computes conserved gene clusters through N-genomes comparison in two phases.…

Computes conserved gene clusters through N-genomes comparison in two phases. MCMuSeC allows to detect conserved gene clusters under flexible evolutionary constraints in a large number of genomes. The…

MicroSyn
Desktop

MicroSyn

Detects microsynteny in adjacent genomic regions surrounding genes in gene…

Detects microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to…

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