I have 3,300 binned contigs (bacterial sequences) that I would like to know the species (where possible) or the least common ancestor explaining what clades each of these bins would be coming from. I understand that MEGAN is designed to do that, however I have my build my own phylogenetic tree and would like to annotate as much as possible clade information for these bins (as specific as I can get). To do that I have predicted all the protein coding genes for each bin and extracted marker genes (ribosomal proteins and elongation factors) from these bins (anywhere between 30 to 80 genes/ bin depending on the size of the genome or completeness of the binning process), and I am blasting these marker genes/proteins (sicne i'm using their protein sequences, I'm pblasting it against the nr database) against the nr database so that later I can use MEGAN or a a tool of that sort to infer taxonomy.
My questions are the following: is there a better tool than MEGAN out there that can infer taxonomy from my sequences? Blasting these marker genes against the nr database would take up a month I think at this rate. Does anyone know any other methods/techniques to do this? I just want to come up with a list that maps my bins to it's most specific taxonomy, be it at the species level, genus level or higher levels, however specific it could get.
Many thanks in advance.