# HISTORY
26 Mar 2016: Updated by: TOUCHUP-v1.15
21 Mar 2016: Updated by: TOUCHUP-v1.14

# molecular_function

# cellular_component

# biological_process

# WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED

# NOTES
bad tree
1/30/2014
This tree seems to have too many disparate things joined together in this tree. The top level node is a duplication node. Under it, are 29 nodes (28 are very general LUCA nodes; the other one is Deuterostomia). The MSA also supports the idea that this tree contains too many things. I cannot find any places that are conserved across the whole tree.
Of the 29 top level nodes, about half have only a few sequences (from 2 to 5). In many places, the branch lengths look very long.
There are several top level nodes that contain groups of sequences with short branch lengths and where the MSA for that group looks good. Well characterized genes (human and/or mouse) within this tree include:
- BBS4 (BBsome complex subunit)
- TTC8 (BBsome complex subunit)
- IFT88 (IFT B complex subunit)
- OGT (protein N-acetylglucosaminyltransferase activity)
There are several other genes that appear to be well conserved in vertebrates, but which are not well annotated for human or mouse:
- TTC13
- TMTC4
- TMTC3
- TMTC1
- TTC18
- TTC34
- TTC6
- TTC7

# REFERENCE
Annotation inferences using phylogenetic trees
The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).