Lately I have issues with blast. Anyway what I want to do could have different and easier process so I welcome any help. I have a list of cow protein sequences(many, about 200 sequences) and I want to identify their orthologs from about 50 vertebrate species. In the end I want to use these orthologs for an indepth evolutionary analysis. With online blast (specifically tblastn against refseq_rna database), I can get a sensible species hits (evolutionarily). With standalone blast running it from a script, different species come out even with a stringent setting in terms of e-values. I don't want Plasmodium or Drosophila sequences to appear in my hits! Is there a way I can set my blast so as to return hits in the order similar to the web blast?
EDIT: Just to give an example, if I query blast with a single gene query, I would get the first hit being Bos taurus (cow) mRNA (which is what is expected), the second may be Bos mutus (Yak) followed by some other species in the ungulate or equiine families. But with standalone blast, I dont get expected species in that order.