Question Regarding Bootstrap

James McInerney james.o.mcinerney at may.ie
Tue Oct 19 10:25:11 EST 1999


> Second, the bootstrap values will not change for a maximum parsimony
> analysis when you add invariable characters; although they can change a
> little using some other methods, like maximum likelihood.  For maximum
> likelihood, the result is not predictable; sometimes the bootstrap values
> will increase, sometimes they will decrease.
> 


Guy,

Just to take issue with one point in your otherwise impeccable answer. 
Bootstrap values can be affected by the inclusion or exclusion of
constant characters for a parsimony analysis.  This will affect the
sampling process.  If you consider this alignment:


species1    acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgttag
species2    acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtaga
species3    acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtaga
species4    acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgttag


There are three parsimony-informative sites, all supporting the same
topology.  By removing the 60 constant sites you will get a bootstrap
value for the internal branch that is 100%.  If you include the constant
sites, you will only get a bootstrap value of 95.4% (you should do about
one million replicates to get a reasonably accurate estimate of the
b'strap value).

So, the inclusion or exclusion of these sites can affect the bootstrap
values.  There are probably better cases, this is just a quick alignment
I put together.

Kindest regards,

James
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