A tree 400MYA in the making: choosing species for a phylogenetic analysis between zebrafish and human genes
As of June of 2018, this is the list of species that have a sequenced genome (at least partially) and I use in phylogenetic and reconciliation analysis focused on investigating genetic evolution between zerbafish and mammals:
Updating Gene Ontology mappings using biomaRt
This is another small R function to download updated Gene Ontology mappings for a set of Ensembl Gene IDs. I use it to obtain the Gene Ontology categories linked to each gene from the zebrafish Zv10 assembly when performing enrichment of a RNAseq in goseq.