Ancestral sequence reconstruction with phangorn

For parsimony analysis of the edge length represent the observed number of changes. Reconstructiong ancestral states therefore defines also the edge lengths of a tree. However there can exist several equally parsimonious reconstructions or states can be ambiguous and therefore edge length can differ. ”MPR” reconstructs the ancestral states for each (internal) node as if the tree would be rooted in that node. However the nodes are not independent of each other. If one chooses one state for a specific node, this can restrict the choice of neighboring nodes (figure 2). The funtion acctran (accelerated transformation) assigns edge length and internal nodes to the tree [3].