jacknifing sites and estimating protein site-rate

James McInerney james.o.mcinerney at may.ie
Wed Oct 4 05:07:53 EST 2000

Andrew Roger wrote:
> Hi,
> 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?

Does PHYLIP-Seqboot not do this?

> 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)?

Does puzzle do this?  It will pump out numbers corresponding to sites
and their categories according to a discrete-gamma distribution.  could
be wrong, but I seem to remember this.

                        (0 0) 
|Dr. James O. McInerney,         Phone +353 1 708 3860          |
|Dept. Biology,                  Fax   +353 1 708 3845          |
|Natl. Univ. Ireland,            Email james.o.mcinerney at may.ie |        
|Maynooth, Co. Kildare, Ireland                                 |
|http://www.may.ie/academic/biology/jmbioinformatics.shtml      |
|http://www.bioinf.org/                                         |
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