The following are most of the data sets and many of the trees that were used as examples in the book. When you click on the download link you may see the data set or tree as text in your browser. If so, then you can save it by using the "Save" or "Save As" choice in the browser's "File" menu. Alternatively, you can mark the text and copy it out of the browser window.
In some cases the data sets are described as simulated on particular trees. The trees will be found below, in the table of trees.
| name | description | link to download it |
| Example data set | This is the simple discrete characters data set used in Table 8.1. It also includes The five species used in Table 1.1 |
example.dat |
| 14-species Primates data set |
This is a 14-species data set with mitochondrial sequences. It was selected by Masami Hasegawa from a data set of sequences of 896 nucleotides collected by a number of researchers in Japan. Hasegawa selected sites from the D-loop noncoding region and third positions of adjacent coding sequences, to achieve a set of sites that was as close as possible to having no rate variation. It is used in Figure 19.1, Table 19.1, and Figure 19.2. |
primates.dna |
| 7-species Primates data set |
This is a 7-species data set which is a subset of the above 14-species subset. It contains only cow, mouse, and 5 species of great apes. It is used in Table 12.1 and Figure 12.3, and in Figures 21.2 and 21.3. |
primates2.dna |
| 7-species Primates distances |
Distances computed from the preceding data set, using the F84 distance with empirical base frequencies and transition/transversion ratio set to 2.0. The file is in the NEXUS format suitable for the program Splitstree. This isrelevant to Table 12.1, Figure 12.3, and the splits table in between them. |
primates.dst |
| Sarich data set | This is a set of immunological distances collected by Vincent Sarich and published in his 1969 paper "Pinniped phylogeny" published in Systematic Zoology 22: 416-422. The values have been averaged across the diagonal to symmetrize them. The data set is used on pages 163-168. |
sarich.dst |
| Example of Kimura 2-parameter model |
The two sequences that are tabulated in Table 13.4. Evolved with a Kimura 2-parameter model with branch length 0.2 between them and transition/transversion ratio 2. |
k2ptable |
| 4-species Hadamard data set |
This is the 4-species data set simulated on the tree described on page 280, using the Jukes-Cantor model. |
hadamard.dna |
| 4-species Hadamard data set (YR) |
This is the same data set, coded as Purine/Pyrimidine
(R and Y). When analyzed using only these states, it gives the Hadamard analysis shown in on pages 280-281 and in Table 17.4. |
hadamard.yr |
| 6-species Hadamard data set |
This is the 6-species data set simulated on the tree shown in Figure 17.1. |
hadamard2.dna |
| 6-species Hadamard data set (YR) |
This is the same data set, coded as Purine/Pyrimidine
(R and Y). When sites are coded into these states, they have the spectrum shown in that Figure. |
hadamard2.yr |
| Two-peak data set | This artificial data set, when analyzed by the Jukes-Cantor method with a molecular clock, gives the profile log-likelihood curves shown in Figure 19.3. |
twopeak.dna |
| Bootstrap example numbers | The histograms of the sample and the three bootstrap samples from that, for the mixture of normal distributions used to explain the bootstrap on page 336 in chapter 20. |
bootexample |
| Numbers for KHT test | The log-likelihood values for the 232 sites used in the table in Figure 21.2, and the differences between them given there and in Figure 21.3. |
khtloglikes khtdiffs |
| Character values and contrasts for example in Comparative Methods chapter |
The two-character data set used to plot Figure 25.3, and the contrasts derived from them and plotted in Figure 25.5 |
twoclades contrasts |
| Fossil example data set | The example data set of present-day and fossil species given in Table 32.1 and used for Figure 32.3. The analysis is described on page 550. |
fossil.dat |
One data set used in the book seems to have been lost, and is therefore not available for download:
Here are some of the trees (aside from the small ones with just a few species) mentioned in the book. They are given in the Newick format. Clicking on the links in the right column will cause them to be displayed on your browser: from there you can save them by selecting the Save or Save As option on your browser's File menu. Alternatively, you can mark the text and copy it out of the browser window.
(More will be put here soon).
| Page | Description | link to tree |
| 166 | UPGMA tree for Sarich carnivore data | sarichupgma.tre |
| 168 | Neighbor-Joining tree for Sarich carnivore data | sarichnj.tre |
| 182 | Trees found in split decomposition example | splitdecomp.tre |
| 260 | Tree for ancestor reconstruction example | ancestor.tre |
| 282 | 6-species tree used to simulate Hadamard example | hadtree6.tre |
| 341 | Five trees for majority-rule consensus example | majorityrule.tre |
| 366 | Two trees for paired sites test example | pairedsites.tre |
| 396 | Tree used to generate Brownian motion example | (to be provided soon) |
| 423 | Example of punctuated equilibrium tree | punctuated.tre |
| 424 | Example of 10 species tree from that tree | punctuated10.tre |
| 430 | Five-species tree used to simulate threshold character | (to be provided soon) |
| 434 | Two-clade tree used to show comparative method problem | compare.tre |
| 458 | Nine random coalescent trees | coalescent.tre |
| 522 | Trees for consensus-tree example | consensus.tre |
| 532 | Trees for tree-distance example | treedistances.tre |
| 566 | Birth-death process trees | bd1.tre bd2.tre |
| 573 | Tree used as example for tree-drawing | drawing.tre |
Those interested in a list of typos and their corrections
for the book should look at the web page here.
A list of reviews of the book that have appeared, and some reactions to them, will be found here.