Whether the estimation of ancestral shapes is done using coordinates of Procrustes aligned specimens or partial warp scores does not matter. One could even base the computations on relative warp scores (if alpha = 0 and the uniform component is included). These all just represent rigid rotations of the same space so they contain the same information about variation among specimens. See, for example, Rohlf, F. J. 1999. Shape statistics: Procrustes superimpositions and tangent spaces. Journal of Classification, 16:197-223.
I do not know the details of how the Rhetenor module performs its computations so I cannot comment about that. I did see a comment on the Mesquite website about assuming all branch lengths were equal when "reconstructing" trees using squared-change parsimony. If so, that would be a major difference. ------------------------ F. James Rohlf, Distinguished Professor Ecology & Evolution, Stony Brook University www: http://life.bio.sunysb.edu/ee/rohlf > -----Original Message----- > From: morphmet [mailto:[EMAIL PROTECTED] > Sent: Thursday, August 23, 2007 4:00 PM > To: morphmet > Subject: TPS tree vs. Mesquite > > Dear morphometers, > > I would like some advice towards detailed documentation on the > algorithms and methods used by TPStree to estimate ancestral > configurations. This is because I want to compare the results of a > module called Rhetenor (E. Dyreson and W. Maddison) in Mesquite (A > modular system for evolutionary analysis by W. Maddison and D. Maddison) > and TPStree. > > I understand TPStree does the estimation of ancestral shapes by working > on partial warps. However, the estimations carried out by Rhetenor seem > to be based on coordinate data only, thus the results between both are > different. > > Thanks for the help provided > > Pablo > > Pablo Jarrin > Grad. Student > Dept. of Biology > Boston University > -- > Replies will be sent to the list. > For more information visit http://www.morphometrics.org -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
