10.5281/zenodo.2542571
https://zenodo.org/records/2542571
oai:zenodo.org:2542571
Patricio, Mateus
Mateus
Patricio
0000-0003-2056-3946
European Bioinformatics Institute
Muffato, Matthieu
Matthieu
Muffato
0000-0002-7860-3560
European Bioinformatics Institute
Rutherford, Kim Matthew
Kim Matthew
Rutherford
0000-0001-6277-726X
University of Cambridge
Gemmell, Neil J.
Neil J.
Gemmell
0000-0003-0671-3637
University of Otago
Ortholog data from the tuatara genome project
Zenodo
2019
tuatara
orthologs
2019-01-24
10.5281/zenodo.2542570
Creative Commons Attribution 4.0 International
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).