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Question Regarding Bootstrap

James McInerney james.o.mcinerney at may.ie
Wed Oct 20 13:32:04 EST 1999

Dr. Mitchell,

The reason I suggested performing a million bootstraps is that the more
bootstraps you perform, the closer you will get to the actual bootstrap
value.  If the support for an internal node is close to either zero or
100 percent, then the variance on this estimate is much lower than if it
is close to 50% (in other words, it asymptotes around 50%).

If you perform only 5 bootstrap replicates, then you will only get a
very poor estimate of the bootstrap support for an internal node.  If
you perform 100 bootstraps, then your estimate is better.  You could
empirically determine the variance for each node, by performing
successive 100-replicate runs and looking at the difference in support
values for each run.

However, by performing one million runs, you have a very _accurate_
estimate of the bootstrap support for any given node.  The variance will
be very small.

For my given case, you could concievably perform 100 runs on the full
dataset and the dataset that only had parsimony-informative sites and
get the same values for each run (100% support).  However, by performing
1,000,000 replicates, you are very unlikely to get this result, unless,
of course there is NO difference between the two answers.

Hope this makes sense.


A Mitchell wrote:
> James McInerney <james.o.mcinerney at may.ie> wrote:
> <snipped>
> > you should do about one million replicates to get a reasonably accurate
> > estimate of the b'strap value
> James,
> Please explain this one!

             Dr. James O. McInerney,
Dept. Biology,                       Dept. Zoology,
Natl. Univ. Ireland,                 The Natural History Museum,
Maynooth,                  and       Cromwell road,
Co. Kildare, Ireland                 London SW7 5BD, UK.
Phone +353 1 708 3860                +44 171 938 9163
Fax   +353 1 708 3845                +44 171 938 9158
email james.o.mcinerney at may.ie       j.mcinerney at nhm.ac.uk

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