homomcl is a C++ implementation of the BLAST similarity graph construction algorithm used by OrthoMCL. It differs from the OrthoMCL algorithm only in that it does not include the Reciprocal Best Hits reweighting step designed to identify orthologous pairwise relationships between sequences. Thus, homomcl produces a similarity graph (in ABC format) where edges represent simple pairwise homology. This graph can be used with MCL to cluster sequences into homologous families.
homomcl <length-file> <e-value> <blast-file>
The input arguments are
<length-file> - A tab-delimited file of all sequence ids and the corresponding sequence lengths
<e-value> - The e-value cutoff used to prune edges from the graph
<blast-file> - A BLAST results file in tabular format (-outfmt 6)