I have two questions:
1) does anyone have/know of a script or small program that allows one to
site-jacknife by randomly removing a user-defined number (or percentage)
of positions in one's alignment. Preferably something that can handle
phylip sequential format?
2) does anyone know of a program that will do an ML estimate of
site-rates in a amino acid alignment, given a tree and a transition
probability matrix (e.g. similar to Olsen's DNArates, but for proteins)?
Any help would be greatly appreciated.
aroger at is.dal.ca