TREECON for Windows user manual

BOOTSTRAP ANALYSIS

Bootstrap analysis can be used to place confidence intervals on phylogenies and is in fact a kind of statistical analysis to test the reliability of certain branches in the evolutionary tree (Efron and Gong, 1983; Felsenstein, 1985; Swofford et al., 1996). It involves resampling one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. In the case of nucleic acid (amino acid) sequences, the resampled data are the nucleotides (amino acids) of a sequence while the statistical significance of a specific cluster is given by the fraction of trees, based on the resampled data, containing that cluster.

When the 'bootstrap' is chosen as an option, the program asks how many bootstrap samples S have to be generated. S vectors of weights are then generated, each with a length C, which is the number of columns in the sequence alignment. These vectors describe the number of times each position is selected. Selection is carried out with the help of a (pseudo)random number generator that chooses C numbers between 1 and C, and whose seed is taken from the time provided by the system. A weight of zero means that the column is dropped from the analysis. A weight of 1 means that the column is counted once, while a weight of 2 means that the column is counted as if it were present two times, and so on (Felsenstein, 1985). All weights add up to a total of C. When the bootstrap samples are generated, S distance matrices are constructed automatically. Bootstrap analysis also implies the automatic construction, rooting and comparison of the S bootstrap trees, which can be chosen from the different menus. Bootstrap values can be displayed on the evolutionary tree afterwards.

If you want to perform bootstrap analysis, make sure that you have enough room on the hard disk to store all your distance matrices. For example, if you want to resample 100 times, 100 distance matrices are stored on the hard-disk. In a next run, the distance matrices, and the unrooted and rooted phylogenies based on the resampled data are deleted automatically.

Bootstrap analysis and rooting trees

An option in the DRAW program is to reroot the tree. With this option the tree can be rooted anywhere and an outgroup of more than one species can be selected. However, in the previous version of TREECON (for DOS), some bootstrap values could be wrong when a tree with bootstrap values was rerooted afterwards. This problem has been solved now but rerooting bootstrapped trees should be done with caution (see Rerooting a tree).

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