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Table 1 Programs included in performance testing

From: Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

Program Version Command line
BLAST 2.2.24 ./blastall -p blastp -F F -C 0 -b 0 -v 10 -a $T -M $M -G $GO
-E $GE -i $Q -d $D
BLAST+ 2.2.24+ ./blastp -seg no -comp_based_stats F -num_alignments 0
-num_descriptions 10 -num_threads $T -matrix $M
-gapopen $GO -gapextend $GE -query $Q -db $D
SWIPE 1.0 ./swipe -v 10 -a $T -M $M.mat -G $GO -E $GE -i $Q -d $D
STRIPED   ./striped -c 10 -T $T -i -$GO -e -$GE $M.mat $Q $D.fsa
SWPS3 20080605 ./swps3 -j $T -i -$GO -e -$GE $M.mat $Q $D.fsa
  1. Command line variables: threads ($T), score matrix file name ($M), gap open ($GO) and extension ($GE) penalties (positive values), query file name ($Q), database file basename ($D)