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altree(1p) r
Analysing phylogeny trees
--permutations|r number
        Number of permutations used to calculate exact p_values (Only for association test)

Related

--tree-to-analyse number With this option, you can specify the tree to use (instead of random). Can be used several times to specify multiple trees.
--s-site-number number Number of the S character site in the sequence (only for localisation method using S-character)

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