Adding external annotation to the phylogeny tree
there are nice features in R ggtree package. You may use the geom_cladelabel() function for your purposes. But I haven't find yet a way to automatize clade annotation. To do it, you have to be sure of the clade homogeneity before removing tiplabs. here are some commands to do clade label annotation:

annot&lt;-read.delim("annota.txt", header = T)

ggtr&lt;-as.treedata(pars.a)
g&lt;-ggtree(ggtr)
#find the node number corresponding to the common ancestor of the top clade in you tree
MRCA(ggtr, "AAL40400", "AAF25519")
#here, check that all accessions belong to the same organism/group
subset(annot, label=="AAL40400" | label=="AAF25519")
#in this case, sequences are related to bovine.
g&lt;-g + geom_cladelabel(node=89, label="Bovine", align=F, fontsize=4)
plot(g)

#another example
MRCA(ggtr, "AAA46456", "AAF97738")
subset(annot, label=="AAA46456" | label=="AAF97738")
g&lt;-g+ geom_cladelabel(node=73, label="Rodent", align=F, fontsize=4)
plot(g)