Synthetic Data
Data.dat contains 16 synthetic DNA sequence alignments of 1000 base
pairs and with two recombinant zones each. The dominant topology is in
State=1, the first recombinant region is in State=2, and the second recombinantion
event switches to State=3. You can find a definition of the three states
by typing
MATLAB> help Tree4
on the MATLAB command line. This also shows
you how the branch-length vectors are defined. The data sets vary with
respect to the branch lengths of the phylogentic tree, the lengths of the
recombination zones, their locations, and the location of the recombination
events in time (in percent of the external branch lengths along which the
sequences have evolved at the time of the event).
Location of the recombinant regions
In the following 5-tupels, the boldface numbers indicate the lengths
of the recombinant zones, while numbers typed in italics indicate
the lengths of the non-recombinant regions.
| 1-4 |
200-200-200-200-200 |
| 5-8 |
200-100-300-300-100 |
| 9-12 |
200-100-500-100-100 |
| 13-16 |
200-50-400-250-100 |
Branch lengths
You find a definition of the branch-length vectors by
typing
MATLAB> help Tree4
at the MATLAB prompt.
| 1-2, 5-6, 9-10, 13-14 |
[0.1 0.1 0.1 0.1 0.2] |
| 3-4, 7-8, 11-12, 15-16 |
[0.05 0.1 0.2 0.1 0.1] |
Time of the recombination event
If the number is even, the recombination event happened after evolving
along 70% of the external branches, if the number is odd, it happened
after evolving along 80% of the external branches.
Last modified: Mon May 22 13:51:27 BST