[Taxacom] SINES, LINES and chromosomal rearrangements (was: contamination)

[Jason Mate]

Ok - I get that. As long as there is character incongruence there ishomoplasy, although if one is limited to two characters then one cannotmake a choice as to which. That still appears to correspond to my pointthat one has to have a tree to identify homoplasious features (and alsodetermine how much of a 'problem' the level of homoplasy depending onthe strength (as measured by whatever indices) of that tree.ANDPerhaps it's my ignorance, but picking the largest set of mutuallycongruent characters seems like it's effectively the same thing as a'tree'. But then I admit my ignorance of the clique analysis algorithmand accept I could be wrong in that assertion.The tree is just the summary (the ´average´) of asking dichotomous questions to the data. It is also much more easily understood than a matrix, even if data is lost in the translation. Character congruence ´is´parsimony, and parsimony is one basic tenets of science. 

Best
Jason