# ========================================================================= # GRAMPA: MUL-tree reconciliation # 04.02.2017 | 01:57:26 # LOG 01.57.26: Number of threads: 2 # LOG 01.57.27: The input species tree with internal nodes labeled: (((B,A)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,D)<6> # LOG 01.57.27: Input species tree is: Singly-labeled # LOG 01.57.27: No H1 node defined Searching all possible H1 nodes. # LOG 01.57.27: No H2 node defined Searching all possible H2 nodes. # LOG 01.57.27: Using gene trees in file: .\gene_trees_18.txt # LOG 01.57.27: Total gene trees: 1000 # LOG 01.57.27: Main results and logs will be written to file: auto_example_output\auto_test_out.txt # LOG 01.57.27: The number of groups for each tree will be calculated: auto_example_output\auto_test_checknums.txt # LOG 01.57.27: Filtered trees will be saved (if necessary): auto_example_output\auto_test_trees_filtered.txt # LOG 01.57.27: Filtering gene trees with # of polyploid groups over: 8 # LOG 01.57.27: Detailed results will be written to file: auto_example_output\auto_test_det.txt # LOG 01.57.27: Detailed output will contain: Reconciliation scores only # LOG 01.57.27: Reconciling to: Singly-labeled and MUL-trees # LOG 01.58.39: Filtered trees: 31 # LOG 01.58.39: Final tree count for reconciliations: 969 # --------- # Tree # H1 node H2 node Tree string Total score ST (((B,A)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,D)<6> 5476 MT-1 A A (((B,(A+,A*)<1>)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6280 MT-2 A C (((B,A+)<1>,(((x,y)<2>,z)<3>,(C,A*)<4>)<5>)<6>,D)<7> 6244 MT-3 A B ((((B,A*)<1>,A+)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6115 MT-4 A D (((B,A+)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,(D,A*)<6>)<7> 6088 MT-5 A <3> (((B,A+)<1>,((((x,y)<2>,z)<3>,A*)<4>,C)<5>)<6>,D)<7> 6420 MT-6 A z (((B,A+)<1>,(((x,y)<2>,(z,A*)<3>)<4>,C)<5>)<6>,D)<7> 7236 MT-7 A <2> (((B,A+)<1>,((((x,y)<2>,A*)<3>,z)<4>,C)<5>)<6>,D)<7> 7353 MT-8 A <1> ((((B,A+)<1>,A*)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6115 MT-9 A y (((B,A+)<1>,(((x,(y,A*)<2>)<3>,z)<4>,C)<5>)<6>,D)<7> 7372 MT-10 A x (((B,A+)<1>,((((x,A*)<2>,y)<3>,z)<4>,C)<5>)<6>,D)<7> 7378 MT-11 A <6> ((((B,A+)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,D)<6>,A*)<7> 6423 MT-12 A <4> (((B,A+)<1>,((((x,y)<2>,z)<3>,C)<4>,A*)<5>)<6>,D)<7> 6375 MT-13 A <5> ((((B,A+)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,A*)<6>,D)<7> 6325 MT-14 C A (((B,(A,C*)<1>)<2>,(((x,y)<3>,z)<4>,C+)<5>)<6>,D)<7> 6455 MT-15 C C (((B,A)<1>,(((x,y)<2>,z)<3>,(C+,C*)<4>)<5>)<6>,D)<7> 5812 MT-16 C B ((((B,C*)<1>,A)<2>,(((x,y)<3>,z)<4>,C+)<5>)<6>,D)<7> 6443 MT-17 C D (((B,A)<1>,(((x,y)<2>,z)<3>,C+)<4>)<5>,(D,C*)<6>)<7> 6069 MT-18 C <3> (((B,A)<1>,((((x,y)<2>,z)<3>,C*)<4>,C+)<5>)<6>,D)<7> 6329 MT-19 C z (((B,A)<1>,(((x,y)<2>,(z,C*)<3>)<4>,C+)<5>)<6>,D)<7> 7233 MT-20 C <2> (((B,A)<1>,((((x,y)<2>,C*)<3>,z)<4>,C+)<5>)<6>,D)<7> 7351 MT-21 C <1> ((((B,A)<1>,C*)<2>,(((x,y)<3>,z)<4>,C+)<5>)<6>,D)<7> 6167 MT-22 C y (((B,A)<1>,(((x,(y,C*)<2>)<3>,z)<4>,C+)<5>)<6>,D)<7> 7371 MT-23 C x (((B,A)<1>,((((x,C*)<2>,y)<3>,z)<4>,C+)<5>)<6>,D)<7> 7377 MT-24 C <6> ((((B,A)<1>,(((x,y)<2>,z)<3>,C+)<4>)<5>,D)<6>,C*)<7> 6398 MT-25 C <4> (((B,A)<1>,((((x,y)<2>,z)<3>,C+)<4>,C*)<5>)<6>,D)<7> 6329 MT-26 C <5> ((((B,A)<1>,(((x,y)<2>,z)<3>,C+)<4>)<5>,C*)<6>,D)<7> 6293 MT-27 B A (((B+,(A,B*)<1>)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6118 MT-28 B C (((B+,A)<1>,(((x,y)<2>,z)<3>,(C,B*)<4>)<5>)<6>,D)<7> 6233 MT-29 B B ((((B+,B*)<1>,A)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6282 MT-30 B D (((B+,A)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,(D,B*)<6>)<7> 6088 MT-31 B <3> (((B+,A)<1>,((((x,y)<2>,z)<3>,B*)<4>,C)<5>)<6>,D)<7> 6419 MT-32 B z (((B+,A)<1>,(((x,y)<2>,(z,B*)<3>)<4>,C)<5>)<6>,D)<7> 7236 MT-33 B <2> (((B+,A)<1>,((((x,y)<2>,B*)<3>,z)<4>,C)<5>)<6>,D)<7> 7353 MT-34 B <1> ((((B+,A)<1>,B*)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6118 MT-35 B y (((B+,A)<1>,(((x,(y,B*)<2>)<3>,z)<4>,C)<5>)<6>,D)<7> 7372 MT-36 B x (((B+,A)<1>,((((x,B*)<2>,y)<3>,z)<4>,C)<5>)<6>,D)<7> 7378 MT-37 B <6> ((((B+,A)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,D)<6>,B*)<7> 6421 MT-38 B <4> (((B+,A)<1>,((((x,y)<2>,z)<3>,C)<4>,B*)<5>)<6>,D)<7> 6383 MT-39 B <5> ((((B+,A)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,B*)<6>,D)<7> 6333 MT-40 D A (((B,(A,D*)<1>)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D+)<7> 6464 MT-41 D C (((B,A)<1>,(((x,y)<2>,z)<3>,(C,D*)<4>)<5>)<6>,D+)<7> 6250 MT-42 D B ((((B,D*)<1>,A)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D+)<7> 6458 MT-43 D D (((B,A)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,(D+,D*)<6>)<7> 5493 MT-44 D <3> (((B,A)<1>,((((x,y)<2>,z)<3>,D*)<4>,C)<5>)<6>,D+)<7> 6436 MT-45 D z (((B,A)<1>,(((x,y)<2>,(z,D*)<3>)<4>,C)<5>)<6>,D+)<7> 7236 MT-46 D <2> (((B,A)<1>,((((x,y)<2>,D*)<3>,z)<4>,C)<5>)<6>,D+)<7> 7353 MT-47 D <1> ((((B,A)<1>,D*)<2>,(((x,y)<3>,z)<4>,C)<5>)<6>,D+)<7> 6263 MT-48 D y (((B,A)<1>,(((x,(y,D*)<2>)<3>,z)<4>,C)<5>)<6>,D+)<7> 7372 MT-49 D x (((B,A)<1>,((((x,D*)<2>,y)<3>,z)<4>,C)<5>)<6>,D+)<7> 7378 MT-50 D <6> ((((B,A)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,D+)<6>,D*)<7> 6315 MT-51 D <4> (((B,A)<1>,((((x,y)<2>,z)<3>,C)<4>,D*)<5>)<6>,D+)<7> 6444 MT-52 D <5> ((((B,A)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,D*)<6>,D+)<7> 6315 MT-53 <3> A (((B,(A,((x*,y*)<1>,z*)<2>)<3>)<4>,(((x+,y+)<5>,z+)<6>,C)<7>)<8>,D)<9> 6441 MT-54 <3> C (((B,A)<1>,(((x+,y+)<2>,z+)<3>,(C,((x*,y*)<4>,z*)<5>)<6>)<7>)<8>,D)<9> 5931 MT-55 <3> B ((((B,((x*,y*)<1>,z*)<2>)<3>,A)<4>,(((x+,y+)<5>,z+)<6>,C)<7>)<8>,D)<9> 6436 MT-56 <3> D (((B,A)<1>,(((x+,y+)<2>,z+)<3>,C)<4>)<5>,(D,((x*,y*)<6>,z*)<7>)<8>)<9> 6018 MT-57 <3> <3> (((B,A)<1>,((((x+,y+)<2>,z+)<3>,((x*,y*)<4>,z*)<5>)<6>,C)<7>)<8>,D)<9> 4807 MT-58 <3> <1> ((((B,A)<1>,((x*,y*)<2>,z*)<3>)<4>,(((x+,y+)<5>,z+)<6>,C)<7>)<8>,D)<9> 5974 MT-59 <3> <6> ((((B,A)<1>,(((x+,y+)<2>,z+)<3>,C)<4>)<5>,D)<6>,((x*,y*)<7>,z*)<8>)<9> 6286 MT-60 <3> <4> (((B,A)<1>,((((x+,y+)<2>,z+)<3>,C)<4>,((x*,y*)<5>,z*)<6>)<7>)<8>,D)<9> 5931 MT-61 <3> <5> ((((B,A)<1>,(((x+,y+)<2>,z+)<3>,C)<4>)<5>,((x*,y*)<6>,z*)<7>)<8>,D)<9> 6068 MT-62 z A (((B,(A,z*)<1>)<2>,(((x,y)<3>,z+)<4>,C)<5>)<6>,D)<7> 6459 MT-63 z C (((B,A)<1>,(((x,y)<2>,z+)<3>,(C,z*)<4>)<5>)<6>,D)<7> 6184 MT-64 z B ((((B,z*)<1>,A)<2>,(((x,y)<3>,z+)<4>,C)<5>)<6>,D)<7> 6453 MT-65 z D (((B,A)<1>,(((x,y)<2>,z+)<3>,C)<4>)<5>,(D,z*)<6>)<7> 6084 MT-66 z <3> (((B,A)<1>,((((x,y)<2>,z+)<3>,z*)<4>,C)<5>)<6>,D)<7> 6067 MT-67 z z (((B,A)<1>,(((x,y)<2>,(z+,z*)<3>)<4>,C)<5>)<6>,D)<7> 6644 MT-68 z <2> (((B,A)<1>,((((x,y)<2>,z*)<3>,z+)<4>,C)<5>)<6>,D)<7> 6067 MT-69 z <1> ((((B,A)<1>,z*)<2>,(((x,y)<3>,z+)<4>,C)<5>)<6>,D)<7> 6243 MT-70 z y (((B,A)<1>,(((x,(y,z*)<2>)<3>,z+)<4>,C)<5>)<6>,D)<7> 7284 MT-71 z x (((B,A)<1>,((((x,z*)<2>,y)<3>,z+)<4>,C)<5>)<6>,D)<7> 7283 MT-72 z <6> ((((B,A)<1>,(((x,y)<2>,z+)<3>,C)<4>)<5>,D)<6>,z*)<7> 6434 MT-73 z <4> (((B,A)<1>,((((x,y)<2>,z+)<3>,C)<4>,z*)<5>)<6>,D)<7> 6348 MT-74 z <5> ((((B,A)<1>,(((x,y)<2>,z+)<3>,C)<4>)<5>,z*)<6>,D)<7> 6354 MT-75 <2> A (((B,(A,(x*,y*)<1>)<2>)<3>,(((x+,y+)<4>,z)<5>,C)<6>)<7>,D)<8> 6449 MT-76 <2> C (((B,A)<1>,(((x+,y+)<2>,z)<3>,(C,(x*,y*)<4>)<5>)<6>)<7>,D)<8> 6109 MT-77 <2> B ((((B,(x*,y*)<1>)<2>,A)<3>,(((x+,y+)<4>,z)<5>,C)<6>)<7>,D)<8> 6443 MT-78 <2> D (((B,A)<1>,(((x+,y+)<2>,z)<3>,C)<4>)<5>,(D,(x*,y*)<6>)<7>)<8> 6081 MT-79 <2> <3> (((B,A)<1>,((((x+,y+)<2>,z)<3>,(x*,y*)<4>)<5>,C)<6>)<7>,D)<8> 5776 MT-80 <2> z (((B,A)<1>,(((x+,y+)<2>,(z,(x*,y*)<3>)<4>)<5>,C)<6>)<7>,D)<8> 5776 MT-81 <2> <2> (((B,A)<1>,((((x+,y+)<2>,(x*,y*)<3>)<4>,z)<5>,C)<6>)<7>,D)<8> 6981 MT-82 <2> <1> ((((B,A)<1>,(x*,y*)<2>)<3>,(((x+,y+)<4>,z)<5>,C)<6>)<7>,D)<8> 6214 MT-83 <2> <6> ((((B,A)<1>,(((x+,y+)<2>,z)<3>,C)<4>)<5>,D)<6>,(x*,y*)<7>)<8> 6425 MT-84 <2> <4> (((B,A)<1>,((((x+,y+)<2>,z)<3>,C)<4>,(x*,y*)<5>)<6>)<7>,D)<8> 6248 MT-85 <2> <5> ((((B,A)<1>,(((x+,y+)<2>,z)<3>,C)<4>)<5>,(x*,y*)<6>)<7>,D)<8> 6322 MT-86 <1> C (((B+,A+)<1>,(((x,y)<2>,z)<3>,(C,(B*,A*)<4>)<5>)<6>)<7>,D)<8> 6221 MT-87 <1> D (((B+,A+)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,(D,(B*,A*)<6>)<7>)<8> 6040 MT-88 <1> <3> (((B+,A+)<1>,((((x,y)<2>,z)<3>,(B*,A*)<4>)<5>,C)<6>)<7>,D)<8> 6394 MT-89 <1> z (((B+,A+)<1>,(((x,y)<2>,(z,(B*,A*)<3>)<4>)<5>,C)<6>)<7>,D)<8> 7233 MT-90 <1> <2> (((B+,A+)<1>,((((x,y)<2>,(B*,A*)<3>)<4>,z)<5>,C)<6>)<7>,D)<8> 7346 MT-91 <1> <1> ((((B+,A+)<1>,(B*,A*)<2>)<3>,(((x,y)<4>,z)<5>,C)<6>)<7>,D)<8> 5817 MT-92 <1> y (((B+,A+)<1>,(((x,(y,(B*,A*)<2>)<3>)<4>,z)<5>,C)<6>)<7>,D)<8> 7372 MT-93 <1> x (((B+,A+)<1>,((((x,(B*,A*)<2>)<3>,y)<4>,z)<5>,C)<6>)<7>,D)<8> 7377 MT-94 <1> <6> ((((B+,A+)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,D)<6>,(B*,A*)<7>)<8> 6347 MT-95 <1> <4> (((B+,A+)<1>,((((x,y)<2>,z)<3>,C)<4>,(B*,A*)<5>)<6>)<7>,D)<8> 6265 MT-96 <1> <5> ((((B+,A+)<1>,(((x,y)<2>,z)<3>,C)<4>)<5>,(B*,A*)<6>)<7>,D)<8> 6265 MT-97 y A (((B,(A,y*)<1>)<2>,(((x,y+)<3>,z)<4>,C)<5>)<6>,D)<7> 6462 MT-98 y C (((B,A)<1>,(((x,y+)<2>,z)<3>,(C,y*)<4>)<5>)<6>,D)<7> 6226 MT-99 y B ((((B,y*)<1>,A)<2>,(((x,y+)<3>,z)<4>,C)<5>)<6>,D)<7> 6456 MT-100 y D (((B,A)<1>,(((x,y+)<2>,z)<3>,C)<4>)<5>,(D,y*)<6>)<7> 6089 MT-101 y <3> (((B,A)<1>,((((x,y+)<2>,z)<3>,y*)<4>,C)<5>)<6>,D)<7> 6340 MT-102 y z (((B,A)<1>,(((x,y+)<2>,(z,y*)<3>)<4>,C)<5>)<6>,D)<7> 7047 MT-103 y <2> (((B,A)<1>,((((x,y+)<2>,y*)<3>,z)<4>,C)<5>)<6>,D)<7> 7128 MT-104 y <1> ((((B,A)<1>,y*)<2>,(((x,y+)<3>,z)<4>,C)<5>)<6>,D)<7> 6260 MT-105 y y (((B,A)<1>,(((x,(y+,y*)<2>)<3>,z)<4>,C)<5>)<6>,D)<7> 7013 MT-106 y x (((B,A)<1>,((((x,y*)<2>,y+)<3>,z)<4>,C)<5>)<6>,D)<7> 7128 MT-107 y <6> ((((B,A)<1>,(((x,y+)<2>,z)<3>,C)<4>)<5>,D)<6>,y*)<7> 6441 MT-108 y <4> (((B,A)<1>,((((x,y+)<2>,z)<3>,C)<4>,y*)<5>)<6>,D)<7> 6414 MT-109 y <5> ((((B,A)<1>,(((x,y+)<2>,z)<3>,C)<4>)<5>,y*)<6>,D)<7> 6376 MT-110 x A (((B,(A,x*)<1>)<2>,(((x+,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6458 MT-111 x C (((B,A)<1>,(((x+,y)<2>,z)<3>,(C,x*)<4>)<5>)<6>,D)<7> 6233 MT-112 x B ((((B,x*)<1>,A)<2>,(((x+,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6452 MT-113 x D (((B,A)<1>,(((x+,y)<2>,z)<3>,C)<4>)<5>,(D,x*)<6>)<7> 6091 MT-114 x <3> (((B,A)<1>,((((x+,y)<2>,z)<3>,x*)<4>,C)<5>)<6>,D)<7> 6319 MT-115 x z (((B,A)<1>,(((x+,y)<2>,(z,x*)<3>)<4>,C)<5>)<6>,D)<7> 7036 MT-116 x <2> (((B,A)<1>,((((x+,y)<2>,x*)<3>,z)<4>,C)<5>)<6>,D)<7> 7136 MT-117 x <1> ((((B,A)<1>,x*)<2>,(((x+,y)<3>,z)<4>,C)<5>)<6>,D)<7> 6251 MT-118 x y (((B,A)<1>,(((x+,(y,x*)<2>)<3>,z)<4>,C)<5>)<6>,D)<7> 7136 MT-119 x x (((B,A)<1>,((((x+,x*)<2>,y)<3>,z)<4>,C)<5>)<6>,D)<7> 7004 MT-120 x <6> ((((B,A)<1>,(((x+,y)<2>,z)<3>,C)<4>)<5>,D)<6>,x*)<7> 6444 MT-121 x <4> (((B,A)<1>,((((x+,y)<2>,z)<3>,C)<4>,x*)<5>)<6>,D)<7> 6417 MT-122 x <5> ((((B,A)<1>,(((x+,y)<2>,z)<3>,C)<4>)<5>,x*)<6>,D)<7> 6370 MT-123 <6> <6> ((((B+,A+)<1>,(((x+,y+)<2>,z+)<3>,C+)<4>)<5>,D+)<6>,(((B*,A*)<7>,(((x*,y*)<8>,z*)<9>,C*)<10>)<11>,D*)<12>)<13> 6328 MT-124 <4> A (((B,(A,(((x*,y*)<1>,z*)<2>,C*)<3>)<4>)<5>,(((x+,y+)<6>,z+)<7>,C+)<8>)<9>,D)<10> 6444 MT-125 <4> B ((((B,(((x*,y*)<1>,z*)<2>,C*)<3>)<4>,A)<5>,(((x+,y+)<6>,z+)<7>,C+)<8>)<9>,D)<10> 6439 MT-126 <4> D (((B,A)<1>,(((x+,y+)<2>,z+)<3>,C+)<4>)<5>,(D,(((x*,y*)<6>,z*)<7>,C*)<8>)<9>)<10> 5916 MT-127 <4> <1> ((((B,A)<1>,(((x*,y*)<2>,z*)<3>,C*)<4>)<5>,(((x+,y+)<6>,z+)<7>,C+)<8>)<9>,D)<10> 6015 MT-128 <4> <6> ((((B,A)<1>,(((x+,y+)<2>,z+)<3>,C+)<4>)<5>,D)<6>,(((x*,y*)<7>,z*)<8>,C*)<9>)<10> 6122 MT-129 <4> <4> (((B,A)<1>,((((x+,y+)<2>,z+)<3>,C+)<4>,(((x*,y*)<5>,z*)<6>,C*)<7>)<8>)<9>,D)<10> 6090 MT-130 <4> <5> ((((B,A)<1>,(((x+,y+)<2>,z+)<3>,C+)<4>)<5>,(((x*,y*)<6>,z*)<7>,C*)<8>)<9>,D)<10> 6015 MT-131 <5> D (((B+,A+)<1>,(((x+,y+)<2>,z+)<3>,C+)<4>)<5>,(D,((B*,A*)<6>,(((x*,y*)<7>,z*)<8>,C*)<9>)<10>)<11>)<12> 6040 MT-132 <5> <6> ((((B+,A+)<1>,(((x+,y+)<2>,z+)<3>,C+)<4>)<5>,D)<6>,((B*,A*)<7>,(((x*,y*)<8>,z*)<9>,C*)<10>)<11>)<12> 6040 MT-133 <5> <5> ((((B+,A+)<1>,(((x+,y+)<2>,z+)<3>,C+)<4>)<5>,((B*,A*)<6>,(((x*,y*)<7>,z*)<8>,C*)<9>)<10>)<11>,D)<12> 6103 # --------- The MUL-tree with the minimum parsimony score is MT-57: (((B,A)<1>,((((x+,y+)<2>,z+)<3>,((x*,y*)<4>,z*)<5>)<6>,C)<7>)<8>,D)<9> Score = 4807 # LOG: Total execution time: 551.504 seconds. # 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