Hi there, I hope one of you guys can help me with this quite basic question.
First of all i am trying to pick out homologs for phylogenetic analysis using standalone blast in the unix terminal. i am using a single gene in fasta format as query against a downloaded genome formatted with formatdb. I get the output i want with this but is there a way i can get my highest scoring hit in a fasta file output?
Secondly when i conduct the same search using the bl2seq command i get very different outputs, with hits much smaller in length (and clearly noise), and when i apply the same e-value constraints as i use with my blastall search, no hits at all.