TRee-based Exploration of Neighborhoods and Domains

Searching for regularities in protein evolution...

Align protein sequences and build a tree

Provide protein sequences and start the analysis or use our embedded id parser. Use a variety of MAFFT alignment algorithms, and FastTree and MEGA tree building options. Reorder the alignment according to the tree leaves.

Identify protein domain architectures

Identify protein domains, transmembrane an d low-complexity regions. Make use of Pfam, COG, KOG, SMART, PRK, TIGR and MiST models.

Identify gene neighborhoods

Identify gene neighborhoods and operons for 125000+ genomes. Set your own distance threshold between the genes in operons. Set the number of neighboring genes to visualize.

Cluster genes

Cluster genes based on identified shared domains of encoded proteins. Customize the number of not shared domains for genes to be clustered.

Visualize results on the tree

Combine the tree and identified domains or gene neighborhoods in one interactive picture. Explore domains and gene neighborhoods. Take advantage of сross-links with Pfam, CDD, NCBI and MiST. Save SVG figure and detailed results of each step.

Bring your own data

If you have your own tree upload it and run subsequent steps. You can optionally upload your alignment to reorder it.