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How do I force PAUP* to use the branch lengths I specify when computing site likelihoods?

April 26, 2017branch computing force lengths likelihoods paup* site specify

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How do I force PAUP* to use the branch lengths I specify when computing site likelihoods?

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Assuming that you have a tree file (for example, “foo.tre”) in which descriptions of trees contain branch length information, you could read in the trees from this file and preserve the branch length information as follows: