Program | Parameters (and abbreviation) | Running time (user and system) in seconds | Memory consumption in Mb |
---|---|---|---|
HSP/MUM determination | |||
NCBI-BLASTN | (ncbiblastn) | 25.79 | 165.92 |
WU-BLASTN | (wublastn) | 896.79 | 904.69 |
BLASTZ | K=2000 (blastz2000) | 48.11 | 125.73 |
K=2500 (blastz2500) | 47.80 | 124.39 | |
K=3000 (blastz3000) | 47.64 | 123.19 | |
K=3500 (blastz3500) | 47.61 | 122.45 | |
BLAT | -minScore=0 − minIdentity=0 − tileSize=8 (blatminTS) | 2,134.54 | 2443.43 |
-minScore=0 − minIdentity=0 (blatmin) | 178.15 | 174.78 | |
-minScore=30 − minIdentity=50 (BLAT) | 177.05 | 167.41 | |
-minScore=30 − minIdentity=90 (blatid90) | 177.08 | 167.41 | |
MUMmer | -l 20 -mum (mum20) | 13.74 | 94.84 |
-l 30 -mum (mum30) | 13.76 | 94.52 | |
-l 40 -mum (mum40) | 13.77 | 94.31 | |
-l 50 -mum (mum50) | 13.72 | 94.17 | |
-l 20 -mumreference (ref20) | 13.80 | 93.44 | |
-l 30 -mumreference (ref30) | 13.81 | 93.44 | |
-l 40 -mumreference (ref40) | 13.79 | 93.44 | |
-l 50 -mumreference (ref50) | 13.75 | 93.44 | |
-l 20 -maxmatch (max20) | 14.07 | 93.44 | |
-l 30 -maxmatch (max30) | 13.95 | 93.44 | |
-l 40 -maxmatch (max40) | 13.86 | 93.44 | |
-l 50 -maxmatch (max50) | 13.88 | 93.44 | |
Distance calculation with GBDP (all formulas in each case) | |||
tr F-2 | mean, all programs | 6,169.98 | 1836.62 |
cov F-2 | 22.22 | 424.68 | |
tr NF | 6,178.77 | 1853.68 | |
cov NF | 22.51 | 404.98 | |
tr F-2 | mean, all programs except MUMmer | 39.54 | 415.04 |
cov F-2 | 12.18 | 229.58 | |
tr NF | 111.19 | 506.07 | |
cov NF | 19.78 | 235.64 | |
tr F-2 | mean, NCBI-BLASTN only | 155.83 | 732.63 |
cov F-2 | 34.89 | 465.39 | |
tr NF | 206.68 | 942.36 | |
cov NF | 43.13 | 473.68 | |
tr F-2 | mean, MUMmer only | 11,278.68 | 3021.26 |
cov F-2 | 30.60 | 587.26 | |
tr NF | 11,235.07 | 2976.68 | |
cov NF | 24.78 | 546.09 |