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 |