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paup*

Question tag: paup* 23 Questions

0 Votes 1 Ans

How do I tell PAUP* to estimate the proportion of invariant sites and and estimate the shape parameter of a discrete, four-category gamma distribution applied to the sites that are not invariant?

discrete estimate invariant parameter paup* proportion shape sites

0 Votes 1 Ans

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

branch computing force lengths likelihoods paup* site specify

0 Votes 1 Ans

For nucleotide models: Is the score that GARLI reports at the end of a run equivalent to what PAUP* would calculate after fully optimizing model parameters and branch lengths on the final topology?

CALCULATE equivalent garli models nucleotide paup* reports run score

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