EUCALYPT: efficient tree reconciliation enumerator

Table 2 Number of solutions found by the programs CORE-PA and EUCALYPT

Dataset	Leaves		Cost vector	Reconciliations
	H	P		CORE-PA			EUCALYPT
				#T	#C	#A	#T	#C	#A	#CA
EC	7	10	〈−1,1,1,1〉	2	0	2	2	0	2	1
			〈0,1,1,0〉	18	0	18	24	0	24	8
GL	8	10	〈−1,1,1,1〉	2	0	2	2	0	2	1
			〈0,1,1,0〉	12	0	12	12	0	12	5
SC	11	14	〈−1,1,1,1〉	1	0	0	1	0	1	1
			〈0,1,1,0〉	82	2	80	113	3	110	18
RP	13	13	〈−1,1,1,1〉	3	1	2	3	1	2	1
			〈0,1,1,0〉	69	25	44	117	45	72	29
SFC	15	16	〈−1,1,1,1〉	40	40	0	40	40	0	0
			〈0,1,1,0〉	1000*	741	259	6332	5069	1263	81
PLML	18	18	〈−1,1,1,1〉	2	0	0	2	0	2	1
			〈0,1,1,0〉	45	2	43	448	28	420	16
PLMP	18	18	〈−1,1,1,1〉	2	0	0	2	0	2	1
			〈0,1,1,0〉	147	0	147	262	0	262	34
RH	34	42	〈−1,1,1,1〉	197	197	0	1056	1056	0	0
			〈0,1,1,0〉	1000*	0	1000	4080384	310284	3770100	275
PP	36	41	〈−1,1,1,1〉	17	0	17	144	0	144	2
			〈0,1,1,0〉	182	8	174	498960	55440	443520	129
FD	20	51	〈−1,1,1,1〉	196	86	110	944	368	576	7
			〈0,1,1,0〉	1000*	1000	0	1.5×10¹⁵	*	*	*
COG2085	100	44	〈−1,1,1,1〉	1000*	0	1000	109056	26496	82560	3
			〈0,1,1,0〉	1000*	0	1000	3.5×10¹¹	*	*	*
COG3715	100	40	〈−1,1,1,1〉	869	869	0	63360	63360	0	0
			〈0,1,1,0〉	1000*	0	1000	1.2×10¹²	*	*	*
COG4964	100	27	〈−1,1,1,1〉	13	13	0	36	36	0	0
			〈0,1,1,0〉	1000*	0	1000	8586842	2603598	5983244	300
COG4965	100	30	〈−1,1,1,1〉	1000*	335	665	44800	13312	31488	5
			〈0,1,1,0〉	1000*	0	1000	907176	387192	519984	208

Number of solutions found by the programs CORE-PA and EUCALYPT for each dataset and each cost vector 〈c _c,c _d,c _s,c _l〉. The columns represent: #T = total number of optimal solutions, #C = total number of cyclic solutions and #A = total number of acyclic solutions. For EUCALYPT the column #CA denotes the number of event classes in the set of acyclic solutions. CORE-PA limits to 1000 the total number of enumerated solutions and these cases are denoted by the symbol ∗. Bold numbers indicate the cases where the number of solutions produced by CORE-PA differs from the one found by EUCALYPT.

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