Table 1 Programs included in performance testing

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