Yeah, that's what I was wondering: to update megablast tool to use NCBI
BLAST+ .

I revised megablast wrapper a bit to use the legacy_blast.pl from NCBI
BLAST+, but it seems the output format is not compatible with the tool
(Fetch taxonomic representation) in metagenomic analyses anymore.

So it looks like the only solution at the moment is to have both NCBI NCBI+
and an old version of BLAST.

Thanks,
Luobin

On Fri, Mar 23, 2012 at 10:55 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Fri, Mar 23, 2012 at 4:36 PM, Luobin Yang <yangl...@isu.edu> wrote:
> > I've noticed these wrappers for BLAST+. I actually was talking about the
> > megablast tool under NGS Mapping section...
> >
> > Thanks,
> > Luobin
>
> Oh - you mean update it to use BLAST+ instead of legacy BLAST
> internally? I asked about this too before writing the BLAST+ wrappers
> and one major concern was about breaking reproducibility - the newer
> BLAST doesn't give identical results.
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003342.html
>
> Also everything the megablast wrapper offers and more is in the blastn
> wrapper.
>
> Peter
>
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