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Command: FastTree -log test.ref.stat test1.aln
FastTree Version 2.1.3 SSE3
Alignment: test1.aln
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
Read 16 sequences, 103 positions
NJ ((VOG0001|NC_015586-YP_004539132.1|:0.08006,VOG0001|NC_021569-YP_008130367.1|:0.06909):0.28343,(VOG0001|HG315669-CDF76785.1|:0.05788,VOG0001|NC_007189-YP_257152.1|:0.05310):0.23598,((VOG0001|AB910602-BAP16707.1|:-0.00331,VOG0001|NC_001396-NP_536673.1|:0.00331):0.27398,(VOG0001|NC_002014-NP_040572.1|:0.22527,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.00364,VOG0001|JF719732-AEQ25512.1|:0.00039):0.23140):0.06056):0.03925);
ME_NNI1 ((VOG0001|NC_015586-YP_004539132.1|:0.08006,VOG0001|NC_021569-YP_008130367.1|:0.06909):0.28343,(VOG0001|HG315669-CDF76785.1|:0.05788,VOG0001|NC_007189-YP_257152.1|:0.05310):0.23598,((VOG0001|AB910602-BAP16707.1|:-0.00331,VOG0001|NC_001396-NP_536673.1|:0.00331):0.27398,(VOG0001|NC_002014-NP_040572.1|:0.22527,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.00364,VOG0001|JF719732-AEQ25512.1|:0.00039):0.23140):0.06056):0.03925);
Min_evolution NNIs converged at round 1 -- skipping some rounds
ME_SPR1 ((VOG0001|NC_015586-YP_004539132.1|:0.08006,VOG0001|NC_021569-YP_008130367.1|:0.06909):0.28343,(VOG0001|HG315669-CDF76785.1|:0.05788,VOG0001|NC_007189-YP_257152.1|:0.05310):0.23598,((VOG0001|AB910602-BAP16707.1|:-0.00331,VOG0001|NC_001396-NP_536673.1|:0.00331):0.27398,(VOG0001|NC_002014-NP_040572.1|:0.22527,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.00364,VOG0001|JF719732-AEQ25512.1|:0.00039):0.23140):0.06056):0.03925);
ME_NNI5 ((VOG0001|NC_015586-YP_004539132.1|:0.08006,VOG0001|NC_021569-YP_008130367.1|:0.06909):0.28343,(VOG0001|HG315669-CDF76785.1|:0.05788,VOG0001|NC_007189-YP_257152.1|:0.05310):0.23598,((VOG0001|AB910602-BAP16707.1|:-0.00331,VOG0001|NC_001396-NP_536673.1|:0.00331):0.27398,(VOG0001|NC_002014-NP_040572.1|:0.22527,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.00364,VOG0001|JF719732-AEQ25512.1|:0.00039):0.23140):0.06056):0.03925);
Min_evolution NNIs converged at round 5 -- skipping some rounds
ME_SPR2 ((VOG0001|NC_015586-YP_004539132.1|:0.08006,VOG0001|NC_021569-YP_008130367.1|:0.06909):0.28343,(VOG0001|HG315669-CDF76785.1|:0.05788,VOG0001|NC_007189-YP_257152.1|:0.05310):0.23598,((VOG0001|AB910602-BAP16707.1|:-0.00331,VOG0001|NC_001396-NP_536673.1|:0.00331):0.27398,(VOG0001|NC_002014-NP_040572.1|:0.22527,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.00364,VOG0001|JF719732-AEQ25512.1|:0.00039):0.23140):0.06056):0.03925);
ME_NNI9 ((VOG0001|NC_015586-YP_004539132.1|:0.08006,VOG0001|NC_021569-YP_008130367.1|:0.06909):0.28343,(VOG0001|HG315669-CDF76785.1|:0.05788,VOG0001|NC_007189-YP_257152.1|:0.05310):0.23598,((VOG0001|AB910602-BAP16707.1|:-0.00331,VOG0001|NC_001396-NP_536673.1|:0.00331):0.27398,(VOG0001|NC_002014-NP_040572.1|:0.22527,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.00364,VOG0001|JF719732-AEQ25512.1|:0.00039):0.23140):0.06056):0.03925);
Min_evolution NNIs converged at round 9 -- skipping some rounds
ME_Lengths ((VOG0001|NC_015586-YP_004539132.1|:0.11474,VOG0001|NC_021569-YP_008130367.1|:0.09524):0.69939,(VOG0001|HG315669-CDF76785.1|:0.08613,VOG0001|NC_007189-YP_257152.1|:0.06680):0.48248,((VOG0001|AB910602-BAP16707.1|:-0.00882,VOG0001|NC_001396-NP_536673.1|:0.00882):0.50579,(VOG0001|NC_002014-NP_040572.1|:0.40382,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.00804,VOG0001|JF719732-AEQ25512.1|:-0.00278):0.39145):0.17543):0.13672);
Total branch-length 3.186 after 0.02 sec
ML_Lengths1 ((VOG0001|NC_015586-YP_004539132.1|:0.13179,VOG0001|NC_021569-YP_008130367.1|:0.09001):0.89356,(VOG0001|HG315669-CDF76785.1|:0.06867,VOG0001|NC_007189-YP_257152.1|:0.07456):0.60898,((VOG0001|AB910602-BAP16707.1|:0.00014,VOG0001|NC_001396-NP_536673.1|:0.00014):0.54185,(VOG0001|NC_002014-NP_040572.1|:0.43498,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.01169,VOG0001|JF719732-AEQ25512.1|:0.00014):0.49619):0.31928):0.28477);
ML_NNI1 ((VOG0001|NC_015586-YP_004539132.1|:0.13369,VOG0001|NC_021569-YP_008130367.1|:0.08964):0.89888,(VOG0001|HG315669-CDF76785.1|:0.07225,VOG0001|NC_007189-YP_257152.1|:0.06992):0.60147,((VOG0001|AB910602-BAP16707.1|:0.00014,VOG0001|NC_001396-NP_536673.1|:0.00014):0.53674,(VOG0001|NC_002014-NP_040572.1|:0.45432,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.01170,VOG0001|JF719732-AEQ25512.1|:0.00014):0.47644):0.31929):0.28906);
TreeLogLk ML_NNI1 -1268.6504 MaxChange 0.0000
NCategories 20
Rates 0.061114 0.083770 0.114826 0.157394 0.215745 0.295727 0.405360 0.555637 0.761626 1.043981 1.431011 1.961523 2.688710 3.685484 5.051787 6.924613 9.491745 13.010579 17.833933 24.445429
SiteCategories 9 8 11 9 8 11 8 11 11 8 10 9 11 10 9 11 9 6 11 10 9 10 9 11 9 8 9 10 11 10 11 8 10 6 12 9 11 10 9 12 10 10 11 9 10 11 9 9 11 9 11 7 9 10 10 8 10 10 7 11 11 7 11 7 11 10 8 10 11 7 10 11 11 10 10 10 7 11 10 12 10 11 8 11 10 12 7 10 8 9 10 10 9 9 7 10 11 10 8 7 10 10 9
ML_NNI2 ((VOG0001|NC_015586-YP_004539132.1|:0.13369,VOG0001|NC_021569-YP_008130367.1|:0.08964):1.03224,(VOG0001|HG315669-CDF76785.1|:0.07225,VOG0001|NC_007189-YP_257152.1|:0.06992):0.70957,((VOG0001|AB910602-BAP16707.1|:0.00014,VOG0001|NC_001396-NP_536673.1|:0.00014):0.65038,(VOG0001|NC_002014-NP_040572.1|:0.45432,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.01170,VOG0001|JF719732-AEQ25512.1|:0.00014):0.52782):0.34847):0.33908);
TreeLogLk ML_NNI2 -1213.2889 MaxChange 0.0000
Turning off heuristics for final round of ML NNIs (converged)
ML_NNI3 ((VOG0001|NC_015586-YP_004539132.1|:0.13535,VOG0001|NC_021569-YP_008130367.1|:0.09173):1.03937,(VOG0001|HG315669-CDF76785.1|:0.08040,VOG0001|NC_007189-YP_257152.1|:0.06083):0.70020,((VOG0001|AB910602-BAP16707.1|:0.00014,VOG0001|NC_001396-NP_536673.1|:0.00014):0.64756,(VOG0001|NC_002014-NP_040572.1|:0.49836,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.01147,VOG0001|JF719732-AEQ25512.1|:0.00014):0.50887):0.34209):0.34692);
TreeLogLk ML_NNI3 -1213.1646 MaxChange 0.0000
ML_Lengths2 ((VOG0001|NC_015586-YP_004539132.1|:0.13336,VOG0001|NC_021569-YP_008130367.1|:0.09299):1.04041,(VOG0001|HG315669-CDF76785.1|:0.08748,VOG0001|NC_007189-YP_257152.1|:0.05695):0.70041,((VOG0001|AB910602-BAP16707.1|:0.00014,VOG0001|NC_001396-NP_536673.1|:0.00014):0.64756,(VOG0001|NC_002014-NP_040572.1|:0.50449,((VOG0001|AB334720-BAF74204.1|:0.0,VOG0001|AB334721-BAF74214.1|:0.0,VOG0001|J02448-AAA32211.1|:0.0,VOG0001|GQ153919-ACY07158.1|:0.0,VOG0001|JF719733-AEQ25522.1|:0.0,VOG0001|JF719734-AEQ25532.1|:0.0,VOG0001|NC_003287-NP_510887.1|:0.0,VOG0001|NC_025824-YP_009111299.1|:0.0):0.01148,VOG0001|JF719732-AEQ25512.1|:0.00014):0.50599):0.34115):0.34752);
TreeLogLk ML_Lengths2 -1213.1491
Total time: 0.27 seconds Unique: 9/16 Bad splits: 0/6
Dist/N**2: by-profile 15.679 (out 0.519) by-leaf 1.654 avg-prof 7.901
Hill-climb: 0 Update-best: 6
NNI: 0 SPR: 0 ML-NNI: 0
Max-lk operations: lk 5038 posterior 739 approximate-posteriors 0.00% star-only 5
TreeCompleted