Ortholog data from the tuatara genome project

This record contains orthology predictions based on the Maker gene annotation
of the tuatara (Sphenodon punctatus) and a set of 25 other species, using the
Ensembl methodology.

See http://doi.org/10.5281/zenodo.1489354 for the Maker annotation in GFF
format.

The files all_trees.emf.gz and all_homologies.tsv.gz contain the phylogenetic
trees (all_trees.emf.gz, in the EMF alignment format) and the derived pairwise
orthologies and paralogies (all_homologies.tsv.gz, in tabular format).

From the phylogenetic trees, sets of 1-to-1 orthologues across all 26 species
were extracted (pure_one2one_orthologies.txt).  Sets of orthologues that span
all the species but include paralogues were reduced to 1 copy per species
using gene order conservation and sequence similarity. This extra dataset is
available in promoted_one2one_orthologies.txt

The main Ensembl entry point for tuatara is:
  http://www.ensembl.org/Sphenodon_punctatus/

This work is supported by Ngatiwai iwi, Allan Wilson Centre, University of
Otago, New Zealand Genomics Limited, Illumina, National eScience
Infrastructure (NeSI NZ).