Clustering Parameters
Parameters
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Value
Cutoff BLAST E-value
Cutoff DP score
Cutoff percent identity
Cutoff PAM distance
Alignment coverage
Alignment coverage for domain splitting
Score cutoff for domain splitting
Similarity measure for orthology
score
pam
Best hit criterion
none
bidirec
unidirec
Cutoff ratio of the score against the best
Score for missing relationships
Clustering Mode
orthology
homology
Cutoff ratio of paralogs for tree splitting
Without domain splitting
Phylogenetically related organisms
none
species
genus
family
order
Overlap ratio (
r
adj1
) for merging adjacent clusters
-
0.5
0.6
0.7
0.8
0.9
1.0
Coverage ratio (
r
adj2
) for absorbing adjacent small clusters
-
0.75
0.8
0.85
0.9
0.95
1
Microbial Genome Database for Comparative Analysis
Questions and comments to: uchiyama@nibb.ac.jp
