TRIBE-MCL achieves best results on the same data set with inflation value 1.2.
However, how to find the right inflation value for the correct resolution of gene families is not intuitively clear.
For example, in TRIBE-MCL [21], the inflation value is an important parameter that controls cluster granularity and thus gene family size.
The two main parameters to tune are the inflation value in case of TRIBE-MCL and the E-value tree-cutoff in case of MC-UPGMA.
We identified parameters that generate the best classification of C. elegans chemosensory gene families, which we found to be E-value threshold = 0.001 and inflation value = 1.2.
We ran TRIBE-MCL with all possible combinations of E-value and inflation value (32 E-values ×39 inflation values = 1,248 runs).
The inflation value was set to 1.3.
MCL was used with an inflation value of 3.
We found that an inflation value of 4.0 and a pre-inflation value of 3.0 best reproduced the known D. melanogaster families.
Groups of orthologous genes were identified by OrthoMCL with an inflation value of 1.5.
For the MCL clustering algorithm we used an inflation value (-I) of 1.5 (OrthoMCL default).
