TreeFam certainly picks up vertebrate genomes from Ensembl as a data source
and my understanding is the Ensembl Genomes will be handled in the same
manner. Treefam haven't made a release for almost a year.
There is some convergence between the Treefam and Ensembl tree 'doing'
systems with reference to the HMM approach but they are independent groups.
So both Treefam and Ensembl Genomes will generate gene trees. Ensembl
Genomes doesn't specifically aim to include all species in all trees like
Treefam rather we aim to have coverage within broad taxonomic groupings
(metazoa, protists, plants, bacteria, fungi etc.) and then a pan-compara
which includes key species from all of the tree of life (a skeletal Treefam
if you want). Another way of viewing this is that Treefam species coverage
is analogous to the combination of metazoa and protists with some outgroups
from fungi and plants.
Due to our resource limitation we are prioritising inclusion of genomes into
Ensembl Metazoa. Genomes which fall within a funded collaboration first and
then the next candidate from a short list of published species. We are keen
for this to be responsive to the community and so if people have wish lists
then could they send them to me (offline from the list - I don't want to get
into trouble). Personally, I have an arthropod leaning and with that scope
in mind the list currently looks like this:
Some of these groups are actively working on the annotation of their genomes
and so we are liaising with them as to when would be the appropriate time to
incorporate the genome and it's updated annotations.
Ensembl Genomes | VectorBase