n= 20
k = 500
contact_edge transmission_factor = 0.5
character transmission_factor = 0.5
gamma i.i.d.: mean 1.0, stddev 0.2

Test 1:	  5% homoplasy, no contact edges, 20% stddev from ultrametric
Test 2:	  5% homoplasy,  1 contact edge , 20% stddev from ultrametric
Test 3:	  5% homoplasy,  2 contact edges, 20% stddev from ultrametric
Test 4:	 10% homoplasy, no contact edges, 20% stddev from ultrametric
Test 5:	 10% homoplasy,  1 contact edge , 20% stddev from ultrametric
Test 6:	 10% homoplasy,  2 contact edges, 20% stddev from ultrametric
Test 7:	  0% homoplasy, no contact edges, 20% stddev from ultrametric
Test 8:	  0% homoplasy,  1 contact edge , 20% stddev from ultrametric
Test 9:	  0% homoplasy,  2 contact edges, 20% stddev from ultrametric 

How to read the report files:

MP Tree #0 Strict consensus tree
MP Tree #1 Majority consensus tree
NJ Tree #0 NJ tree
UP Tree #0 UPGMA tree

Tree # 0 17 20 fn:(11.8, 5.9) fp:(11.8, 3.4)
Tree has 17 interior edges and 20 taxa
There are 2 network trees
      fn distance to network tree 1 is 11.8%
      fp distance to network tree 1 is 11.8%
      fn distance to network tree 2 is 5.9%
      fp distance to network tree 2 is 3.4%

Quick Summary

Test1		FN %	FP %
MP Strict	4.72	1.18
MP Majority	4.72	1.18
NJ		5.31	5.31
UP		7.67	7.67

Test2		FN %			FP %
MP Strict	19.38, 9.43, 10.61	16.46, 6.49, 7.67
MP Majority	19.38, 9.43, 10.61	16.46, 6.49, 7.67
NJ		18.19, 10.61, 8.84	18.19, 10.61, 8.84
UP		31.17, 27.64, 28.22	31.17, 27.64, 28.22

Test3		FN %						FP %
MP Strict	22.9, 12.9, 18.2, 20.0, 10.0, 15.3, 12.9,  8.2	20.0, 10.0, 15.3, 17.0,  7.1, 12.4, 10.0,  5.3
MP Majority	22.3, 11.8, 17.6, 20.0,  9.4, 15.3, 12.4,  7.7	20.6, 10.0, 15.9, 18.2,  7.7, 13.5, 10.6,  5.9
NJ		23.5, 12.9, 17.6, 21.2, 10.6, 14.7, 16.5, 10.6	23.5, 12.9, 17.6, 21.2, 10.6, 14.7, 16.5, 10.6
UP		20.0, 12.4, 17.6, 23.5, 15.9, 21.1, 12.4, 10.0	20.0, 12.4, 17.6, 23.5, 15.9, 21.1, 12.4, 10.0

Test4		FN %	FP %
MP Strict	18.8	 9.4
MP Majority	17.6	10.6
NJ		20.6	20.6
UP		28.2	28.2

Test5		FN %			FP %
MP Strict	17.6, 27.0, 19.4	11.8, 21.2, 13.5
MP Majority	17.6, 27.0, 19.4	11.8, 21.2, 13.5
NJ		16.5, 27.0, 20.0	16.5, 27.0, 20.0
UP		17.0, 25.9, 18.2	17.0, 25.9, 18.2

Test6		FN %				FP %
MP Strict	 4.1,  7.7, 17.1, 21.7, 19.4	 4.1,  7.7, 17.1, 21.7, 19.4
MP Majority	 4.1,  7.7, 17.1, 21.7, 19.4	 4.1,  7.7, 17.1, 21.7, 19.4
NJ		 8.2, 14.1, 16.5, 22.3, 20.6	 8.2, 14.1, 16.5, 22.3, 20.6
UP		 5.3,  7.7, 17.1, 21.1, 20.0	 5.3,  7.7, 17.1, 21.1, 20.0

Test7		FN %	FP %
MP Strict	 3.0	 0.0
MP Majority	 3.0	 0.0
NJ		 8.8	 8.8
UP		17.6	17.6

Test8		FN %			FP %
MP Strict	13.0,  8.3,  4.1	10.0,  5.3,  1.2
MP Majority	13.0,  8.3,  4.1	10.0,  5.3,  1.2
NJ		16.5,  9.4,  8.3	16.5,  9.4,  8.3
UP		12.9, 14.1,  9.4	12.9, 14.1,  9.4

Test9		FN %			FP %
MP Strict	22.3, 14.1, 14.7	10.0,  1.8,  2.4	
MP Majority	20.6, 12.4, 13.0	11.8,  3.5,  4.1
NJ		25.9, 17.1, 18.8	25.9, 17.1, 18.8
UP		40.0, 28.2, 34.1	40.0, 28.2, 34.1