SHOOT: Phylogenetic gene search and ortholog inference (bioRxiv)
BLAST (basic local alignment search tool) is more than 30 years old, and most readers have probably had the opportunity to BLAST a sequence. BLAST takes an input sequence and searches databases for closely related sequences. However, this tool uses only sequence information to find close matches. Hypothetically, two sequences that have very different origins but have converged on the same sequence would show up as a match – useful, but perhaps implying a close evolutionary relationship that they don’t share. Here, Emms and Kelly present SHOOT, where you can “sprout a branch on the tree of life“. SHOOT queries pre-constructed phylogenetic datsbases (you can search all life, or select just plants) so it’s fast and provides you with a “phylogenetic tree with your query sequence grafted into it“. SHOOT is provided for use at www.shoot.bio. Grab your favorite amino acid sequence and try it! (Note that when I used this I had to edit out all spaces from my amino acid sequence manually.) This will be an excellent tool for teaching, too! (Summary by Mary Williams @PlantTeaching) bioRxiv
