Bootstrap a pairwise distance matrix

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Bio_Ing_Sapienza
Bio_Ing_Sapienza on 24 Aug 2019
Answered: Shubh Sahu on 27 Aug 2019
Hi! I have to bootstrap a distance matrix to have the reliability of my phylogenetic tree. I found bootstrp as matlab function but I am not certain about what to do
%e.g. let us suppose that I have this matrix
M=magic(6);
% Just to have an idea
[bootstat,bootsam]=bootstrp(1000,@fun,M);
%I don't know what kind of fucntion can be correct
I there anyone with some experience in boot strapping a distancematrix for phylogeny?
Thank you in advance
  1 Comment
Adam Danz
Adam Danz on 24 Aug 2019
Bootstrapping involves taking many randomized subsamples of your data, performing the same statistic or function on each subsample, and then analyzing the distribution of results. For example, if you want confidence intervals on the median value of some distribution, you should take randomized subsamples of the population, compute and store the median of the subpopulation, and repeat the process many times until you have a distribution of median values. In that example, @fun would be @median.
Let's say your distance matrix is computed by your homemade function,
output = computePhyloDistance(input)
then your @fun would be @computePhyloDistance.
Step through some of the examples provided by Matlab and the process will become clear.

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Answers (1)

Shubh Sahu
Shubh Sahu on 27 Aug 2019
Hi,
Adding to Adam Danz, Bootstrapping is a random sampling conducted with replacement. It is straight forward way to derive estimates of standard error and confidence intervals for complex estimators of complex parameters of the distribution.
Here is the link you can refer to:

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