How is the topology of a tree curated?
Manual curation is a key feature of TreeFam. During curation, experts manually correct errors in the automatic trees for TreeFam-B families. To curate a tree, the curator gathers phylogenetic and functional information on the genes in the family from journal articles; from manually curated databases such as UniProt, FlyBase, WormBase and OMIM; and from accepted species taxonomy in the NCBI database. If the phylogenetic tree for a family differs from that expected from functional information, published articles or the accepted species taxonomy, the curator explores the plausibility of alternative tree topologies using a combination of published and in-house tools. For example, the Jalview alignment editor is used to display and edit alignments; and an extended version of the ATV tree viewer is used to display and edit phylogenetic trees. If a curator suspects that a tree is missing genes, BLAST and HMMER are run with non-stringent E-value cutoffs, to search for distant sequence matches.
