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Table 2. Command line parameters for similarity search tools as used by the web server. Recommended parameters are in bold.

From: Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

Similarity search tool Command line parameter
NCBI BLAST blastall -p blastn -i QUERY -d SUBJECT -m 7 -a 1 -S 3 -e 10 -F ‘m D’ -b 100000
WU-BLAST blastn SUBJECT QUERY mformat=7 cpus=1 E=10 wordmask=dust B=100000 hspmax=100000 hspsepSmax=50 hspsepQmax=50
BLAT blat SUBJECT QUERY OUTFILE -t=dna -q=dna -out=blast -minScore=30 -minIdentity=50
BLASTZ blastz QUERY SUBJECT B=2 C=2 K=3500 Y=700
Mummer mummer -b -c -F -l 44 -mum SUBJECT QUERY