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.
James
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|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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