Aequatus, an open-source web-based tool developed at Earlham Institute (EI) to visualise homologous gene
structures among differing species or subtypes of a common species. Aequatus works on top of the
Ensembl Compara and Core database schema.
Aequatus uses precalculated gene family information and genomic alignments data in the form of
CIGAR strings, from Ensembl Compara, and cross-references these sequences to Ensembl Core
databases for each species to gather genomic feature information via stable_ids. Aequatus then
processes the comparative and feature data to provide a visual representation of the
phylogenetic and structural relationships among the set of chosen species.
The ultimate goal of the Aequatus is to provide a unique and informative way to render
and explore complex relationships between genes from various species at a level that has so far
License: GPL V3
When you start Aequatus it starts with a blank screen with chromosomal view on top and Gene view.
Two option to start with:
- Choose a gene from gene view
- Search for Gene of interest in either of search box and choose gene from list.
For the purpose of changing reference genome. Reference Genome can be set from the dropdown on
For the purpose of selecting reference chromosome. Select on any of the chromosome karyotype from
Select Reference Gene:
For the purpose of selecting reference gene. Select on any of the gene from Gene view or for
gene of interest search
for gene with
Here Aequatus visualises Homologous genes with phylogenetic tree.
Homologous gene view shows shared exons with smae colour in all genes structure. insertion and
Homologous geneview shows shared exons insertion and deletions.
Here we have various controls to change settings of Aequatus like, toggle view, search, change label
with this control chromosome view can be show or hide, to get more area to display homologous view.
With chromosome view
Without chromosome view
Aequatus has few options to controls to alter visuals of homologous view.
- Toggle Alignment elements (match, insertions, deletions)
- Toggle gene lable between gene info or stable id
Controls -> Label -> Stable Id
Genes with stable id as label
Controls -> Label -> Gene Info
Genes with gene info as label
- Toggle gene view between original or fixed intron length
Controls -> Inrons -> Without
Genes with fixed intron size
Controls -> Inrons -> With
Genes with normal intron size
In Aequatus search can be done from either of the search boxes, any keywords can be used for search
like Accession no., stable id, functionality, etc.
Aequatus has a hard-link REST API for easy access to genes of interest, making it simple to share
information and visualisations with collaborators.
This will directly load homologous view of the gene
This will search for the term in databases and show results
This will directly jump to the species and reference chromosome
Changing Reference Gene
In Aequatus main homologous gene view, Reference gene is the main selected gene, on which other
genes alignments are mapped on, Any other gene from view can be used as reference gene by clicking
on it and click on tree icon in pop-up.
How to setup
Table of content
- Setting up
- Installing and running Aequatus Browser
- Properties file
- Standard features
- Database config
Aequatus Browser requires
- Running Apache Tomcat,
- Ensembl Compara and
- Core MySQL databases,
- Aequatus package from GitHub
- Properties files browser.properties and db.properties (supllied with Aequatus package)
- Maven 3.0
- Java 1.7
Installing and running Aequatus Browser
You will need Maven 3.x.x to build Aequatus. Once you have grabbed the
code and installed Maven, in the root of the project (you should see a pom.xml file and module
directories like browser-web and core etc) call:
mvn clean install -Dprofile=<profile-name> -Dprofile-path=<property-file-path>
It will generate a aequatus-browser.war file copy it to Apache Tomcat webapps and start the
Aequatus Browser should be running at http://<server-path>/
Aequatus Browser property file contains many features those can be changed in browser straight away
browser.title = Demo
- you can set the Web Page Title from here
browser.header = Aequatus Browser Demo
- you can set the Web Page Header from here
browser.urlpath = Aequatus-browser
- you can set the Web Page URL path from here
- i.e. Aequatus-browser-new will be http://<server-path>/Aequatus-browser-new
- jdbc driver - Don't change
- Mysql server location followed by database name