Good survey of approaches for detecting homologous chromosomal segments. No mention of algorithms for conserved gene clusters.
** Conserved gene order Dot plot of gene homology matrix (GHM) constructed using BLAST
Wolfe1997 used GHM to find duplicated segments in yeast.
ADHoRe algorithm has two parameters, the maximum gap size and minimum quality factor.
Other methods include FISH and LineUp.
** Conserved gene content