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Table 1 Software included in performance testing

From: Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

Software Version Command Line
BLAST 2.2.26 blastall -p blastp -F F -C 0 -b 0 -v 10 -a $T -M $M -G $O -E $E -i $Q -d $D
BLAST+ 2.2.31+ blastp -seg no -comp_based_stats F -num_alignments 0 -num_descriptions 10 -num_threads $T -matrix $M -gapopen $O -gapextend $E -query $Q -db $D
SWIPE 2.0.11 swipe -v 10 -a $T -M $M -G $O -E $E -i $Q -d $D
libssa 29 October 2015 libssa_example -c 10 -N $T -M $M -O $O -E $E -t SW -b 16 -s AVX2 -i $Q -d $D
opal 16 November 2015 opal_aligner -x 1 -a SW -o $O -e $E -m $M -s $Q $D
SSW 30 July 2015 test_ssw -x -t $T -o $O -e $E -m $M -f $D -q $Q
Parasail 12 August 2015 parasail_aligner -x -a $A -t $T -o $O -e $E -m $M -f $D -q $Q
  1. Command line variables: threads ($T), score matrix file name ($M), gap open ($O) and extension ($E) penalties (positive values), query file name ($Q), database file basename ($D), Parasail alignment function name ($A)