# ========================================================================= # GRAMPA: MUL-tree reconciliation # 04.02.2017 | 02:17:44 # LOG 02.17.44: Number of threads: 2 # LOG 02.17.45: The input species tree with internal nodes labeled: ((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,D)<6> # LOG 02.17.45: Input species tree is: Singly-labeled # LOG 02.17.45: No H1 node defined Searching all possible H1 nodes. # LOG 02.17.45: No H2 node defined Searching all possible H2 nodes. # LOG 02.17.45: Using gene trees in file: .\gene_trees_33.txt # LOG 02.17.45: Total gene trees: 1000 # LOG 02.17.45: Main results and logs will be written to file: nop_example_output\nop_test_out.txt # LOG 02.17.45: The number of groups for each tree will be calculated: nop_example_output\nop_test_checknums.txt # LOG 02.17.45: Filtered trees will be saved (if necessary): nop_example_output\nop_test_trees_filtered.txt # LOG 02.17.45: Filtering gene trees with # of polyploid groups over: 8 # LOG 02.17.45: Detailed results will be written to file: nop_example_output\nop_test_det.txt # LOG 02.17.45: Detailed output will contain: Reconciliation scores only # LOG 02.17.45: Reconciling to: Singly-labeled and MUL-trees # LOG 02.18.37: Filtered trees: 1 # LOG 02.18.37: Final tree count for reconciliations: 999 # --------- # Tree # H1 node H2 node Tree string Total score ST ((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,D)<6> 4115 MT-1 A A ((((((x,y)<1>,z)<2>,B)<3>,(A+,A*)<4>)<5>,C)<6>,D)<7> 4423 MT-2 A C ((((((x,y)<1>,z)<2>,B)<3>,A+)<4>,(C,A*)<5>)<6>,D)<7> 4753 MT-3 A B ((((((x,y)<1>,z)<2>,(B,A*)<3>)<4>,A+)<5>,C)<6>,D)<7> 4929 MT-4 A D ((((((x,y)<1>,z)<2>,B)<3>,A+)<4>,C)<5>,(D,A*)<6>)<7> 4754 MT-5 A <3> (((((((x,y)<1>,z)<2>,B)<3>,A*)<4>,A+)<5>,C)<6>,D)<7> 4965 MT-6 A z ((((((x,y)<1>,(z,A*)<2>)<3>,B)<4>,A+)<5>,C)<6>,D)<7> 5047 MT-7 A <2> (((((((x,y)<1>,z)<2>,A*)<3>,B)<4>,A+)<5>,C)<6>,D)<7> 5096 MT-8 A <1> (((((((x,y)<1>,A*)<2>,z)<3>,B)<4>,A+)<5>,C)<6>,D)<7> 5113 MT-9 A y ((((((x,(y,A*)<1>)<2>,z)<3>,B)<4>,A+)<5>,C)<6>,D)<7> 5088 MT-10 A x (((((((x,A*)<1>,y)<2>,z)<3>,B)<4>,A+)<5>,C)<6>,D)<7> 5120 MT-11 A <6> (((((((x,y)<1>,z)<2>,B)<3>,A+)<4>,C)<5>,D)<6>,A*)<7> 5055 MT-12 A <4> (((((((x,y)<1>,z)<2>,B)<3>,A+)<4>,A*)<5>,C)<6>,D)<7> 4965 MT-13 A <5> (((((((x,y)<1>,z)<2>,B)<3>,A+)<4>,C)<5>,A*)<6>,D)<7> 4975 MT-14 C A ((((((x,y)<1>,z)<2>,B)<3>,(A,C*)<4>)<5>,C+)<6>,D)<7> 4909 MT-15 C C ((((((x,y)<1>,z)<2>,B)<3>,A)<4>,(C+,C*)<5>)<6>,D)<7> 4370 MT-16 C B ((((((x,y)<1>,z)<2>,(B,C*)<3>)<4>,A)<5>,C+)<6>,D)<7> 4943 MT-17 C D ((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C+)<5>,(D,C*)<6>)<7> 4726 MT-18 C <3> (((((((x,y)<1>,z)<2>,B)<3>,C*)<4>,A)<5>,C+)<6>,D)<7> 5067 MT-19 C z ((((((x,y)<1>,(z,C*)<2>)<3>,B)<4>,A)<5>,C+)<6>,D)<7> 5048 MT-20 C <2> (((((((x,y)<1>,z)<2>,C*)<3>,B)<4>,A)<5>,C+)<6>,D)<7> 5115 MT-21 C <1> (((((((x,y)<1>,C*)<2>,z)<3>,B)<4>,A)<5>,C+)<6>,D)<7> 5113 MT-22 C y ((((((x,(y,C*)<1>)<2>,z)<3>,B)<4>,A)<5>,C+)<6>,D)<7> 5090 MT-23 C x (((((((x,C*)<1>,y)<2>,z)<3>,B)<4>,A)<5>,C+)<6>,D)<7> 5121 MT-24 C <6> (((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C+)<5>,D)<6>,C*)<7> 5039 MT-25 C <4> (((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C*)<5>,C+)<6>,D)<7> 4979 MT-26 C <5> (((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C+)<5>,C*)<6>,D)<7> 4979 MT-27 B A ((((((x,y)<1>,z)<2>,B+)<3>,(A,B*)<4>)<5>,C)<6>,D)<7> 4840 MT-28 B C ((((((x,y)<1>,z)<2>,B+)<3>,A)<4>,(C,B*)<5>)<6>,D)<7> 4813 MT-29 B B ((((((x,y)<1>,z)<2>,(B+,B*)<3>)<4>,A)<5>,C)<6>,D)<7> 4554 MT-30 B D ((((((x,y)<1>,z)<2>,B+)<3>,A)<4>,C)<5>,(D,B*)<6>)<7> 4774 MT-31 B <3> (((((((x,y)<1>,z)<2>,B+)<3>,B*)<4>,A)<5>,C)<6>,D)<7> 4988 MT-32 B z ((((((x,y)<1>,(z,B*)<2>)<3>,B+)<4>,A)<5>,C)<6>,D)<7> 5041 MT-33 B <2> (((((((x,y)<1>,z)<2>,B*)<3>,B+)<4>,A)<5>,C)<6>,D)<7> 4988 MT-34 B <1> (((((((x,y)<1>,B*)<2>,z)<3>,B+)<4>,A)<5>,C)<6>,D)<7> 5107 MT-35 B y ((((((x,(y,B*)<1>)<2>,z)<3>,B+)<4>,A)<5>,C)<6>,D)<7> 5090 MT-36 B x (((((((x,B*)<1>,y)<2>,z)<3>,B+)<4>,A)<5>,C)<6>,D)<7> 5121 MT-37 B <6> (((((((x,y)<1>,z)<2>,B+)<3>,A)<4>,C)<5>,D)<6>,B*)<7> 5086 MT-38 B <4> (((((((x,y)<1>,z)<2>,B+)<3>,A)<4>,B*)<5>,C)<6>,D)<7> 5000 MT-39 B <5> (((((((x,y)<1>,z)<2>,B+)<3>,A)<4>,C)<5>,B*)<6>,D)<7> 5027 MT-40 D A ((((((x,y)<1>,z)<2>,B)<3>,(A,D*)<4>)<5>,C)<6>,D+)<7> 4920 MT-41 D C ((((((x,y)<1>,z)<2>,B)<3>,A)<4>,(C,D*)<5>)<6>,D+)<7> 4848 MT-42 D B ((((((x,y)<1>,z)<2>,(B,D*)<3>)<4>,A)<5>,C)<6>,D+)<7> 4946 MT-43 D D ((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,(D+,D*)<6>)<7> 4217 MT-44 D <3> (((((((x,y)<1>,z)<2>,B)<3>,D*)<4>,A)<5>,C)<6>,D+)<7> 5103 MT-45 D z ((((((x,y)<1>,(z,D*)<2>)<3>,B)<4>,A)<5>,C)<6>,D+)<7> 5050 MT-46 D <2> (((((((x,y)<1>,z)<2>,D*)<3>,B)<4>,A)<5>,C)<6>,D+)<7> 5123 MT-47 D <1> (((((((x,y)<1>,D*)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D+)<7> 5117 MT-48 D y ((((((x,(y,D*)<1>)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D+)<7> 5090 MT-49 D x (((((((x,D*)<1>,y)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D+)<7> 5121 MT-50 D <6> (((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,D+)<6>,D*)<7> 5052 MT-51 D <4> (((((((x,y)<1>,z)<2>,B)<3>,A)<4>,D*)<5>,C)<6>,D+)<7> 5105 MT-52 D <5> (((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,D*)<6>,D+)<7> 5052 MT-53 <3> A ((((((x+,y+)<1>,z+)<2>,B+)<3>,(A,(((x*,y*)<4>,z*)<5>,B*)<6>)<7>)<8>,C)<9>,D)<10> 4767 MT-54 <3> C ((((((x+,y+)<1>,z+)<2>,B+)<3>,A)<4>,(C,(((x*,y*)<5>,z*)<6>,B*)<7>)<8>)<9>,D)<10> 4632 MT-55 <3> D ((((((x+,y+)<1>,z+)<2>,B+)<3>,A)<4>,C)<5>,(D,(((x*,y*)<6>,z*)<7>,B*)<8>)<9>)<10> 4659 MT-56 <3> <3> (((((((x+,y+)<1>,z+)<2>,B+)<3>,(((x*,y*)<4>,z*)<5>,B*)<6>)<7>,A)<8>,C)<9>,D)<10> 4880 MT-57 <3> <6> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A)<4>,C)<5>,D)<6>,(((x*,y*)<7>,z*)<8>,B*)<9>)<10> 4871 MT-58 <3> <4> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A)<4>,(((x*,y*)<5>,z*)<6>,B*)<7>)<8>,C)<9>,D)<10> 4767 MT-59 <3> <5> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A)<4>,C)<5>,(((x*,y*)<6>,z*)<7>,B*)<8>)<9>,D)<10> 4745 MT-60 z A ((((((x,y)<1>,z+)<2>,B)<3>,(A,z*)<4>)<5>,C)<6>,D)<7> 4894 MT-61 z C ((((((x,y)<1>,z+)<2>,B)<3>,A)<4>,(C,z*)<5>)<6>,D)<7> 4832 MT-62 z B ((((((x,y)<1>,z+)<2>,(B,z*)<3>)<4>,A)<5>,C)<6>,D)<7> 4860 MT-63 z D ((((((x,y)<1>,z+)<2>,B)<3>,A)<4>,C)<5>,(D,z*)<6>)<7> 4777 MT-64 z <3> (((((((x,y)<1>,z+)<2>,B)<3>,z*)<4>,A)<5>,C)<6>,D)<7> 5013 MT-65 z z ((((((x,y)<1>,(z+,z*)<2>)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4762 MT-66 z <2> (((((((x,y)<1>,z+)<2>,z*)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4980 MT-67 z <1> (((((((x,y)<1>,z*)<2>,z+)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4980 MT-68 z y ((((((x,(y,z*)<1>)<2>,z+)<3>,B)<4>,A)<5>,C)<6>,D)<7> 5080 MT-69 z x (((((((x,z*)<1>,y)<2>,z+)<3>,B)<4>,A)<5>,C)<6>,D)<7> 5106 MT-70 z <6> (((((((x,y)<1>,z+)<2>,B)<3>,A)<4>,C)<5>,D)<6>,z*)<7> 5098 MT-71 z <4> (((((((x,y)<1>,z+)<2>,B)<3>,A)<4>,z*)<5>,C)<6>,D)<7> 5062 MT-72 z <5> (((((((x,y)<1>,z+)<2>,B)<3>,A)<4>,C)<5>,z*)<6>,D)<7> 5057 MT-73 <2> A ((((((x+,y+)<1>,z+)<2>,B)<3>,(A,((x*,y*)<4>,z*)<5>)<6>)<7>,C)<8>,D)<9> 4702 MT-74 <2> C ((((((x+,y+)<1>,z+)<2>,B)<3>,A)<4>,(C,((x*,y*)<5>,z*)<6>)<7>)<8>,D)<9> 4737 MT-75 <2> B ((((((x+,y+)<1>,z+)<2>,(B,((x*,y*)<3>,z*)<4>)<5>)<6>,A)<7>,C)<8>,D)<9> 4759 MT-76 <2> D ((((((x+,y+)<1>,z+)<2>,B)<3>,A)<4>,C)<5>,(D,((x*,y*)<6>,z*)<7>)<8>)<9> 4709 MT-77 <2> <3> (((((((x+,y+)<1>,z+)<2>,B)<3>,((x*,y*)<4>,z*)<5>)<6>,A)<7>,C)<8>,D)<9> 4759 MT-78 <2> <2> (((((((x+,y+)<1>,z+)<2>,((x*,y*)<3>,z*)<4>)<5>,B)<6>,A)<7>,C)<8>,D)<9> 4920 MT-79 <2> <6> (((((((x+,y+)<1>,z+)<2>,B)<3>,A)<4>,C)<5>,D)<6>,((x*,y*)<7>,z*)<8>)<9> 4993 MT-80 <2> <4> (((((((x+,y+)<1>,z+)<2>,B)<3>,A)<4>,((x*,y*)<5>,z*)<6>)<7>,C)<8>,D)<9> 4806 MT-81 <2> <5> (((((((x+,y+)<1>,z+)<2>,B)<3>,A)<4>,C)<5>,((x*,y*)<6>,z*)<7>)<8>,D)<9> 4905 MT-82 <1> A ((((((x+,y+)<1>,z)<2>,B)<3>,(A,(x*,y*)<4>)<5>)<6>,C)<7>,D)<8> 4850 MT-83 <1> C ((((((x+,y+)<1>,z)<2>,B)<3>,A)<4>,(C,(x*,y*)<5>)<6>)<7>,D)<8> 4809 MT-84 <1> B ((((((x+,y+)<1>,z)<2>,(B,(x*,y*)<3>)<4>)<5>,A)<6>,C)<7>,D)<8> 4817 MT-85 <1> D ((((((x+,y+)<1>,z)<2>,B)<3>,A)<4>,C)<5>,(D,(x*,y*)<6>)<7>)<8> 4775 MT-86 <1> <3> (((((((x+,y+)<1>,z)<2>,B)<3>,(x*,y*)<4>)<5>,A)<6>,C)<7>,D)<8> 4911 MT-87 <1> z ((((((x+,y+)<1>,(z,(x*,y*)<2>)<3>)<4>,B)<5>,A)<6>,C)<7>,D)<8> 4899 MT-88 <1> <2> (((((((x+,y+)<1>,z)<2>,(x*,y*)<3>)<4>,B)<5>,A)<6>,C)<7>,D)<8> 4899 MT-89 <1> <1> (((((((x+,y+)<1>,(x*,y*)<2>)<3>,z)<4>,B)<5>,A)<6>,C)<7>,D)<8> 4932 MT-90 <1> <6> (((((((x+,y+)<1>,z)<2>,B)<3>,A)<4>,C)<5>,D)<6>,(x*,y*)<7>)<8> 5094 MT-91 <1> <4> (((((((x+,y+)<1>,z)<2>,B)<3>,A)<4>,(x*,y*)<5>)<6>,C)<7>,D)<8> 4997 MT-92 <1> <5> (((((((x+,y+)<1>,z)<2>,B)<3>,A)<4>,C)<5>,(x*,y*)<6>)<7>,D)<8> 5037 MT-93 y A ((((((x,y+)<1>,z)<2>,B)<3>,(A,y*)<4>)<5>,C)<6>,D)<7> 4900 MT-94 y C ((((((x,y+)<1>,z)<2>,B)<3>,A)<4>,(C,y*)<5>)<6>,D)<7> 4840 MT-95 y B ((((((x,y+)<1>,z)<2>,(B,y*)<3>)<4>,A)<5>,C)<6>,D)<7> 4927 MT-96 y D ((((((x,y+)<1>,z)<2>,B)<3>,A)<4>,C)<5>,(D,y*)<6>)<7> 4784 MT-97 y <3> (((((((x,y+)<1>,z)<2>,B)<3>,y*)<4>,A)<5>,C)<6>,D)<7> 5060 MT-98 y z ((((((x,y+)<1>,(z,y*)<2>)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4974 MT-99 y <2> (((((((x,y+)<1>,z)<2>,y*)<3>,B)<4>,A)<5>,C)<6>,D)<7> 5035 MT-100 y <1> (((((((x,y+)<1>,y*)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D)<7> 5000 MT-101 y y ((((((x,(y+,y*)<1>)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4886 MT-102 y x (((((((x,y*)<1>,y+)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D)<7> 5000 MT-103 y <6> (((((((x,y+)<1>,z)<2>,B)<3>,A)<4>,C)<5>,D)<6>,y*)<7> 5109 MT-104 y <4> (((((((x,y+)<1>,z)<2>,B)<3>,A)<4>,y*)<5>,C)<6>,D)<7> 5084 MT-105 y <5> (((((((x,y+)<1>,z)<2>,B)<3>,A)<4>,C)<5>,y*)<6>,D)<7> 5074 MT-106 x A ((((((x+,y)<1>,z)<2>,B)<3>,(A,x*)<4>)<5>,C)<6>,D)<7> 4898 MT-107 x C ((((((x+,y)<1>,z)<2>,B)<3>,A)<4>,(C,x*)<5>)<6>,D)<7> 4839 MT-108 x B ((((((x+,y)<1>,z)<2>,(B,x*)<3>)<4>,A)<5>,C)<6>,D)<7> 4917 MT-109 x D ((((((x+,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,(D,x*)<6>)<7> 4789 MT-110 x <3> (((((((x+,y)<1>,z)<2>,B)<3>,x*)<4>,A)<5>,C)<6>,D)<7> 5045 MT-111 x z ((((((x+,y)<1>,(z,x*)<2>)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4944 MT-112 x <2> (((((((x+,y)<1>,z)<2>,x*)<3>,B)<4>,A)<5>,C)<6>,D)<7> 5003 MT-113 x <1> (((((((x+,y)<1>,x*)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4951 MT-114 x y ((((((x+,(y,x*)<1>)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4951 MT-115 x x (((((((x+,x*)<1>,y)<2>,z)<3>,B)<4>,A)<5>,C)<6>,D)<7> 4943 MT-116 x <6> (((((((x+,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,D)<6>,x*)<7> 5114 MT-117 x <4> (((((((x+,y)<1>,z)<2>,B)<3>,A)<4>,x*)<5>,C)<6>,D)<7> 5075 MT-118 x <5> (((((((x+,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,x*)<6>,D)<7> 5072 MT-119 <6> <6> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,C+)<5>,D+)<6>,((((((x*,y*)<7>,z*)<8>,B*)<9>,A*)<10>,C*)<11>,D*)<12>)<13> 5054 MT-120 <4> C ((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,(C,((((x*,y*)<5>,z*)<6>,B*)<7>,A*)<8>)<9>)<10>,D)<11> 4660 MT-121 <4> D ((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,C)<5>,(D,((((x*,y*)<6>,z*)<7>,B*)<8>,A*)<9>)<10>)<11> 4558 MT-122 <4> <6> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,C)<5>,D)<6>,((((x*,y*)<7>,z*)<8>,B*)<9>,A*)<10>)<11> 4707 MT-123 <4> <4> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,((((x*,y*)<5>,z*)<6>,B*)<7>,A*)<8>)<9>,C)<10>,D)<11> 4900 MT-124 <4> <5> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,C)<5>,((((x*,y*)<6>,z*)<7>,B*)<8>,A*)<9>)<10>,D)<11> 4660 MT-125 <5> D ((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,C+)<5>,(D,(((((x*,y*)<6>,z*)<7>,B*)<8>,A*)<9>,C*)<10>)<11>)<12> 4760 MT-126 <5> <6> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,C+)<5>,D)<6>,(((((x*,y*)<7>,z*)<8>,B*)<9>,A*)<10>,C*)<11>)<12> 4760 MT-127 <5> <5> (((((((x+,y+)<1>,z+)<2>,B+)<3>,A+)<4>,C+)<5>,(((((x*,y*)<6>,z*)<7>,B*)<8>,A*)<9>,C*)<10>)<11>,D)<12> 4877 # --------- The tree with the minimum parsimony score is the singly-labled tree (ST): ((((((x,y)<1>,z)<2>,B)<3>,A)<4>,C)<5>,D)<6> Score = 4115 # LOG: Total execution time: 286.153 seconds. # =========================================================================