diff --git a/setup.py b/setup.py
index 50217b4..9f1215f 100644
--- a/setup.py
+++ b/setup.py
@@ -24,6 +24,7 @@
     entry_points={
         'console_scripts': ['soi = soi.options:main',
 							'soi-syn = soi.mcscan:main',
+							'soi-orth = soi.OrthoFinder:main',
         ],
     },
 )
diff --git a/soi/dot_plotter.py b/soi/dot_plotter.py
index 0018c6b..b5ba0f8 100755
--- a/soi/dot_plotter.py
+++ b/soi/dot_plotter.py
@@ -62,6 +62,7 @@ def dotplot_args(parser):
 	group_orth.add_argument('--ofdir', metavar='FOLDER/FILE', type=str, nargs='+', default=None, help="OrthoFinder output folder/ OrthoMCL output pair file. [default=%(default)s]")
 	group_orth.add_argument('--of-ratio', metavar='FLOAT', type=float, default=0, help="Orthology Index cutoff [default=%(default)s]")
 	group_orth.add_argument('--of-color', action='store_true', default=None, help="coloring dots by Orthology Index [default=%(default)s]")
+#	group_orth.add_argument('--use-frac',  action='store_true', default=False, help="use fractionation rate [default=%(default)s]")
 
 	group_ks = parser.add_argument_group('Ks plot', 'options to histogram plot with Ks')
 	group_ks.add_argument('--kaks', metavar='FILE', type=str, default=None, help="kaks output from KaKs_Calculator/WGDI. [default=%(default)s]")
@@ -148,7 +149,7 @@ def main(args):
 	same_sp = True if chrs1 == chrs2 else False
 	blocks, lines1, lines2, ortholog_graph,chrs1, chrs2, d_offset1, d_offset2 = parse_collinearity(
 		collinearity, gff, chrs1, chrs2, kaks, args.homology, 
-		source = args.source, 
+		source = args.source, use_frac=args.use_frac,
 		ofdir=args.ofdir, of_ratio=args.of_ratio, of_color=args.of_color,
 		hide_blocks = args.hide_blocks, use_median=args.use_median, 
 		lower_ks=args.lower_ks, upper_ks=args.upper_ks,
@@ -607,7 +608,7 @@ def parse_gff(gff, chrs1, chrs2):
 
 def parse_collinearity(collinearity, gff, chrs1, chrs2, kaks, homology, 
 		hide_blocks=None, use_median=False, lower_ks=None, upper_ks=None,
-		cluster=False, diagonal=False, gene_axis=False, source=None, 
+		cluster=False, diagonal=False, gene_axis=False, source=None, use_frac=False, 
 		ofdir=None, of_ratio=0, of_color=False, tandem_dist=None, min_block=None,
 		matrix=None, min_same_block=None, **ks_args):
 	blocks = XCollinearity(collinearity, orthologs=ofdir, gff=gff, kaks=kaks, homology=homology, source=source, **ks_args)
@@ -660,6 +661,8 @@ def parse_collinearity(collinearity, gff, chrs1, chrs2, kaks, homology,
 #			pairs = { tuple(sorted(x)) for x in rc.pairs}
 #			intersect = pairs & ortholog_pairs
 			ratio = rc.oi #1.0*len(intersect) / len(pairs)
+			if use_frac:
+				ratio = rc.fractionation_rate(both=True)
 			if not ratio > of_ratio:
 				continue
 			if of_color:
diff --git a/soi/mcscan.py b/soi/mcscan.py
index 541499b..0e11436 100644
--- a/soi/mcscan.py
+++ b/soi/mcscan.py
@@ -611,6 +611,19 @@ def parse_genes(self, genes1,genes2):
 		except KeyError:
 			self.start2, self.end2, self.length2 = None, None, None
 			self.istart2, self.iend2 = None, None
+	def fractionation_rate(self, ref=None, both=False):
+		sp1, sp2 = self.species1, self.species2
+		is1, ie1 = self.istart1, self.iend1
+		is2, ie2 = self.istart2, self.iend2
+		if ref is not None:
+			if ref not in {sp1, sp2}:
+				return None
+			elif ref == sp2:
+				is1, ie1, is2, ie2 = is2, ie2, is1, ie1
+		l1, l2 = ie1 - is1 + 1, ie2-is2+1
+		if both:
+			return 2.0*self.N / (l1+l2)
+		return 1.0*rc.N / l1
 	@property
 	def good_ks(self):
 		return [ks for ks in self.ks if ks is not None]