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    diamond blastp produce longer alignments with lower identity than ncbi blast

    Thanks! Does the only way to set higher penalty for mismatches is via custom matrices? Thanks
  2. B

    diamond blastp produce longer alignments with lower identity than ncbi blast

    Hi all, I'm using diamond blastp as a (great) alternative for blastp, mainly in order to save time. Although I made efforts to make the alignment with similar parameters as much as possible I find that in most of the cases ncbi blast will prefer smaller alignment length (with higher identity)...
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