kcranston
commented
8 years ago Not quite sure what feature you are requesting. The OTU mapping allows you to map a tip to a taxon at any taxonomic level. Are you requesting that you also be allowed to map an internal node in a phylogeny to a taxonomy? That's an interesting idea - it would allow us to capture cases where the phylogeny is suggesting a different circumscription of a higher taxon than suggested by taxonomy or other phylogenies. Right now, we would simply fail to annotate that internal node due to mismatch.
Would it be possible to annotate nodes with taxonomy (higher-level names that are not reflected in the terminal names). Almost all phylogenies take a what we call 'exemplar approach' (Prendini 2001, http://www.jstor.org/stable/3070843?seq=1#page_scan_tab_contents). The terminals form clades which correspond to taxonomic entities (in the Linnaean classification system). It is these clades or taxonomic entities that we are interested in, not the individual terminals. And once we have these nodes annotated with taxonomy, we can also compare multiple trees and point to specific taxonomic entities to identify congruence and conflicts.