The utility is called deco.exe in Windows distribution or simply deco in Linux distribution. Distributions are offered in 32-bit and 64-bit versions.

Deco can load SMILES and MDL (Symyx) Molfiles from the given directory. It can also read molecules from SDfile (sdf). The results are stored in Molfiles and SDfiles.

The program help message is the following:

Usage:
  deco [options] molfiles
Perfoms molecule scaffold detection and R-group deconvolution
Input molecule formats: MOL, SMILES, or SDF
Options:
-h         print this help message
-a         use approximate searching algorithm for scaffold detection
-d <file>  perform R-group deconvolution with scaffold loaded from file
-o <file>  write resulting highlighted molecules to file [default: "deconv.sdf"]
-r <file>  write resulting divided scaffolds and r-groups to file
-s <file>  write maximum obtained scaffold to molfile
-S <file>  write all found scaffolds to SD-file
-I <path>  input directory [default: the current directory]
-O <path>  output directory [default: the current directory]
-na        no aromatic consideration
-l <file>  write detailed log

Examples:

> deco *.mol 
read input molecules from the files "*.mol";
write highlighted molecules to "deconv.sdf"

> deco -s scaf.mol -O out/ m.mol ms.sdf
read molecules from "m.mol" and "ms.sdf";
write maximum scaffold to "out/scaf.mol";
write highlighted molecules to "out/deconv.sdf"

> deco -I out -d scaf.mol -r rg.sdf -o res.sdf -S scafs.sdf ms.sdf 
read scaffold from "out/scaf.mol", write deconvoluton result for molecules in 
"ms.sdf" to "res.sdf" and R-groups to "rg.sdf" and all scaffolds to "scafs.sdf"