Full package name: mesquite.coalesce.RecCoalescenceHistory.RecCoalescenceHistory Duty: Reconstructs a taxon association history (mesquite.assoc.lib.ReconstructAssociation)
Module Explanation
Reconstructs a contained tree within a containing tree so as to minimize the amount of deep coalescence (failure of lineage sorting). The contained tree is assumed to be rooted.
Author(s): Wayne P. Maddison and David R. Maddison
Version 3.70
Commands of Reconstruct Deep Coalescence
toggleReconstruct
Explanation: Sets whether or not the containing tree reconstructor attempts to reconstruct ancestral containing nodes, or finds containing node information already in the history
Parameters: [on = reconstruct; off]
toggleUnrooted
Explanation: Sets whether or not the contained tree is treated as unrooted
Parameters: [on = unrooted; off]
toggleUseLengths
Explanation: Sets whether or not any branch lengths of the contained tree are used in fitting it into the containing tree
Parameters: [on = use lengths; off]
toggleResolve
Explanation: Sets whether or not polytomies in the contained tree are auto-resolved to minimize deep coalescences
