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Embarassingly irreproducible
It is absolutely impossible for someone to reproduce this analysis given the scripts that I have provided.
Issue with logmap2.jar
$ `java -jar logmap2.jar example_tree_0.txt example_tree_1.txt`
0.5
(((t4:0.1670793,t2:0.2363061):1.4368894,t1:0.0593689):0.0587942,(t5:0.0089958,t3:0.8621474):0.0587942);
((t1:0.0593689,t5:0.0089958):0.0000000,((t4:0.1670793,t2:0.2363061):1.4368894,t3:0.8621474):0.0000000);
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