  Summary: TreeGrafter is a new software tool for annotating protein sequences
using annotated phylogenetic trees. Cur-rently, the tool provides annotations
to Gene Ontology terms, and PANTHER protein class, family and subfamily. The
ap-proach is generalizable to any annotations that have been made to internal
nodes of a reference phylogenetic tree. Tree-Grafter takes each input query
protein sequence, finds the best matching homologous family in a library of
pre-calculated, pre-annotated gene trees, and then grafts it to the best
location in the tree. It then annotates the sequence by propagating
anno-tations from its ancestral nodes in the reference tree. We show that
TreeGrafter outperforms subfamily HMM scoring for cor-rectly assigning
subfamily membership, and that it produces highly specific annotations of GO
terms based on annotated reference phylogenetic trees. This method will be
further inte-grated into InterProScan, enabling an even broader user
com-munity.
  Availability: TreeGrafter is freely available on the web at
https://github.com/haimingt/TreeGrafting.
