jacknifing sites and estimating protein site-rate

Andrew Roger aroger at is.dal.ca
Tue Oct 3 13:38:01 EST 2000


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.

Andrew Roger
aroger at is.dal.ca


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