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There The following parameters are available:
Substitution model parameters - selection a selection of the Markov model of substitution:
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Number of substitution rate categories - number the number of substitution rate categories.
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Branch support parameters - the selection of the method that is used to measure branch support:
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Tree searching parameters - the selection of the tree topology searching algorithm:
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Set number of random starting tree - the number of random starting tree.
Optimize tree topology - the tree topology is optimised in order to maximise the likelihood.
Optimize branch lengths - optimize branch lengths.
Optimise substitution rate - substitution rate parameters are optimized.
Display tree in new window - displays tree in the new window.
Display tree with alignment editor - displays tree with alignment editor.
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