[emboss-dev] Enquiry about emboss needleall program
pmr at ebi.ac.uk
Fri Jul 22 08:48:17 UTC 2011
On 07/22/2011 09:18 AM, Tae-Kyung Kim wrote:
> Fortunately, I have found the solution by googling as soon as sending email
> to you.
> sol)./needleall -asequence a.seq -bsequence b.seq -nobrief -gapopen 10
> -gapextend 0.5 -stdout -auto *-aformat3 srspair*
> I am satisfied with much better performance than single needle after testing
> with following test program.
You can simply use -aformat (if there is only one alignment output there
is no need for the parameter number 3) to avoid confusion when you tray
another application with a different number of parameters.
We are also happy to add new alignment formats if anyone needs a
different output format. Any new alignment format will be available to
all alignment outputs (but can be declared as only for pairwise/multiple
or nucleotide/protein alignments)
Happy to be able to help.
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