I am trying to retrieve all the orthologs and paralogs for all fungi species in ensembl fungi database, but I couldn't find a way to download them in bulk. I know Biomart provides the service for manual collection but it doesn't work for my purpose.
For example, I would like to download all ORTHOLOGUES from http://fungi.ensembl.org for Aspergillus clavatus genes (TIGR), is there an easy way to do this in a batch? Furthermore, I fancy getting all orthologs for all fungi species.
BTW, I could see it seems that many of the species have been lost in the ORTHOLOGUES page of Biomart service. For instance, Hyphopichia burtonii NRRL Y-1933, Laccaria amethystina LaAM-08-1.......In fact, there are 735 species listed in the http://fungi.ensembl.org/species.html but only 51 species could be found in the ortholog page? Where are the remaining species?