1. Aequatus Browser, an open-source web-based tool developed at TGAC 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 Browser 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 been unrealised. Aequatus

2. Controls SearchGenomes Chromosomes Navigation Panel Gene Members Homologous View Overview Main window of Aequatus contains various components to search genes, select gene and species and control homologous view, which are annotated in the image below:

3. Aequatus Browser Homologous View Insertions Deletions Shared Exon Shared exons within or between species are shown with same colour Insertsions in shared exons are shown with black blocks and deletions with carat (v) on top Visualising homologous genes with phylogenetic tree.

4. Search Term Previous Search Retrieve results by just clicking on it Result matching search term Showing Gene location, description, stable_id, and direct link to the homologous gene view Search

5. Toggle visuals of match, insertions, deletions, and UTRs from homologous view Toggle label between stable_id and gene info Toggle between actual intron size or fixed length intron view Settings

6. Legends Showing event happened in evolution with colour coded nodes

7. RestAPI Aequatus has a hard-link REST API for easy access to genes of interest, making it simple to share information and visualisations with collaborators. Example – http://…/index.jsp?query=AT1G01710.1 This will directly load homologous view of the gene – http://…/index.jsp?search=AT1G0171 This will search for the term in databases and show results – http://…/index.jsp?ref=arabidopsis_thaliana&chr=4 This will directly jump to the species and reference chromosome

8. For any kind of enquiry about Aequatus please contact us: – Anil.Thanki@tgac.ac.uk Anil.Thanki@tgac.ac.uk – Robert.Davey@tgac.ac.uk Robert.Davey@tgac.ac.uk Aequatus contact