Chris Lewis at the U of S



Email: Christopher Lewis

Bootstrapping

A short "as I understand it" description of bootstraping.
This page assumes you've read the previous links on phylogenetics.


What does the definition mean?

As I understand it from the above definition and various examples on the web (I never found one that I thought was entirely clear so I haven't provided a link to any), bootstraping is randomly modifying bases in the sequences and seeing how this affects the phylogentic tree produced.

       +---+---+                  -------------------
       |       |                  |  A  |  B  |  C  |
       |       |                 A|  \  | 20  | 30  |  
       |   +---+---+              |------------------
       |   |       |             B|  20 |  \  | 15  |
       |   |       |              |------------------
       A   B       C             C|  30 | 15  |  \  |
                                  -------------------

Figure 1 - Phylogentic Tree and table of evolutionary distances

Assume you have a phylogenetic tree and table of evolutionary distances as in Figure 1. During bootstrapping, you would randomly modify bases in sequences A, B and C and see what effect this had on the phylogenetic tree. To do this, you would recalculate the distance matrix with the randomly modified sequences and rebuild the tree. If the tree now branches differently then there is a lesser probability of this being the correct tree.

This process would be repeated some number of times (say 1000) and probabilities would be assigned to each branch based on the number of times that branch occured over the 1000 iterations (Figure 2). The idea is to find out which branches are questionable because the sequences involved are so closely related that some small number of random changes will alter the branching order.

    .70+---+---+                  -------------------
       |       |                  |  A  |  B  |  C  |
       |       |.87              A|  \  | 20  | 30  |  
       |   +---+---+              |------------------
       |   |       |             B|  20 |  \  | 15  |
       |   |       |              |------------------
       A   B       C             C|  30 | 15  |  \  |
                                  -------------------

Figure 2 - Phylogenetic Tree with weighted branches

A Work in Progress