ARB : phylip bootstrapped tree
The following movies show how to make bootstrapped neighbor joining trees using partial aligned sequences.
One can make a distance+neighbor joining in arb using several of the tree menu options, but the bootstrap analysis is done by exporting exactly the same sequences and running a series of phylip programs.
In this example, a subset of the sequences in the tree are used, first to create a phylip bootstrapped tree called outfile in the example (files Bootstrap1.m4v and Bootstrap2.m4v). The numbers in that tree can be added to a neighbor joining tree created by arb (file Neighbor.m4v) that is exported to a postscript file using the tree print menu and edited using a graphics/image manipulation programs (Adobe Illustrator, Canvas, etc.).
We use version 3.6 of phylip, that has different output names for treefiles (outtree instead of treefile), and therefore I had to manually import the tree. Most folks will not have this problem, as they will use the phylip programs that came with arb.
Since it is assumed that the tree is constructed from partial sequences, a filter containing positions where bases are more common than gaps, and excluding ambiguities is setup prior to the analysis using the create SAI/position variability menu, and is used to select positions for analysis.
It is very important to make sure that the same sequences, and same sequence positions (same filter) are used to make the non-bootstrapped tree containing distances, and the bootstraps.