jacknifing sites and estimating protein site-rate
joe at evolution.genetics.washington.edu
Wed Oct 4 14:52:06 EST 2000
In article <8rfqer$gvu$1 at mercury.hgmp.mrc.ac.uk>,
Andrew Roger <aroger at is.dal.ca> wrote:
>> > 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?
>Yes Seqboot does this, but the last time I checked it does a mandatory 50%
>site removal. What I want is to be able to vary the number of sites that I
>can remove by percentage or simple numbers. Trivial but frustrating for a
>non-programmer like me!!!
In SeqBoot version 3.5c change the lines starting at line 715 from:
if (randum(seed) < 0.5)
q = (newgroups - 1.0) / 2;
q = (newgroups + 1.0) / 2;
q = newgroups / 2.0;
to, if you want to delete a fraction, say 0.4,
if (randum(seed) < 0.4)
q = (newgroups - 1.0) * 0.6;
q = (newgroups + 1.0) * 0.6;
q = newgroups * 0.6;
(The 0.6 is, of course, there because it is 1 - 0.4).
I haven't tried this but it should work.
Joe Felsenstein joe at genetics.washington.edu
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
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