Dataset associated to "Annotation matters: the effect of structural gene annotation on orthology"

Dataset including the input and output files in "Annotation matters: the effect of structural gene annotation on orthology".

Input proteomes for OMA and their corresponding splice files are in the OMAproteomes zipped folder. The OMA results for each annotation method are in the zipped folders with the method name (e.g. Augustus.zip).

The fasta files (proteomes) are the same for OrthoFinder input in the cases of UniProt and Augustus (as they only have one isoform per gene). In these cases, the OrthoFinder folders (e.g. OFUniProt.zip), include the OrthoFinder output for that proteomes set. For Ensembl and NCBI, given the different approach each orthology method follows, the specific orthofinder proteomes are also included in the OrthoFinder (OF) zipped folder (e.g. OFtopNCBI.zip), in their corresponding primary_transcripts subfolder. 

The folder GSTDBenchmarOutput.zip contains the results from the Generalized Species Tree Discordance Benchmark.

topNCBI/topEnsembl correspond to the original proteomes downloaded from the databases.

priNCBI/primEnsembl correspond to the proteomes sets which include only the genes found on the primary assembly (reference sequences).

For the species code to species name correspondance, please check the Code-Species.csv file.