> 1. Unit, generally: We have made minor edits throughout the 
>    text to improve clarity and phrasing. Please review carefully 
>    to check that the correct meaning has been retained.

OK, if not indicated otherwise in the corrections.

> 2. Unit Introduction, 2nd and subsequent paragraphs: We have edited 
>    these paragraphs for clarity. Please check they are OK.

OK, if not indicated otherwise in the corrections.

> 3. Basic Protocol 1 Necessary Resources, “Files”: Please note that 
>    since the sample data set EF.phy is included with the software 
>    download, there is no need to post it on the CP Web site.

I was aware of that even in the first edition. However, I was
explicitely requested that all files used in the exercises are
also stored on Wiley's CPBI home page.

It's your decision to change that. I don't mind at all.

> 4. Basic Protocol 1, 
>    (a) step 2: OK to change “MS-DOS” prompt to “Command Prompt.” 
>        Windows has not provided an actual DOS interface since v. 3.1 and 
>        the mention of that program makes the text seem outdated.

No problem. I didn't change that in the corrections. (Please note, that 
in German MS Windows versions the Command prompt is still called
"MS-DOS Eingabeaufforderung" = MS-DOS prompt ;)

>    (b) step 7: Can you recommend a good universal model to try first?

Added in the corrections:
TREE-PUZZLE tries to determine a suitable model by comparing their 
amino acid frequencies with that of the data set.

>    (c) step 7, 2nd annotation: Please explain what you mean by “
>        ...can be restricted to even more different models...”

Added in the corrections:
...by explicitly setting the GTR substitution parameters...

>    (c) step 8, 2nd annotation: Please suggest a good starting model, if any.

Hard to do. One might use the default (HKY) or run ModelTest as indicated 
with the references to 6.5.


> 5. Figure 6.6.3: Correct that the reference for GTR should be Lanave 
>    et al. (1984). It said 1980 in the original.

1984 is correct.

> 6. Basic Protocol 2 introduction, 4th sentence: Please explain what 
>    the quartet support method is used for.

There is no "quartet support method" that was mis-phrased during
copy-editing. It is likelihood mapping with grouped sequences.
It utilizes the numbers of quartets that do or do not support
a certain scenario. I changed words to indicate that in the 
corrections.

> 7. Basic Protocol 2, step 1: We have cross-referenced steps of 
>    Basic Protocol 1, instead of repeating text. Please confirm that 
>    this is OK.

I urge you to revert this as indicated in the corrections,
because this is a very important point I often get emails about
since people are not use commandlines... and they often do not
check such cross-refernces. I accept to add the cross-reference
for the working directory problem (as also done in Protocol 3).

> 8. Support Protocol 2, 
>    (a) step 2 and annotation: Should the users copy the executable 
>    file(s) to the executable binary path? Please clarify.]

Yes, added in the corrections.

> 9. Guidelines for Understanding Results, 
>    (a) Likelihood Mapping for Data Quality and Quartet Support of 
>        Clusters (see Basic Protocol 2)”, 3rd from last paragraph: 
>        We have re-worded the sentence starting “If many dots....” 
>        as it was incomplete in the submitted manuscript. Please check 
>        we have retained the correct meaning and edit as necessary. 
>        As this is the first mention of the term “dots, please explain 
>        what they represent in Figure 6.6.11 and 6.6.12.

The re-wording was OK, but I substituted 'together' by 'joint' and
'dots' by 'points' since that was what they were named in the text 
before.

>    (b)“Comparison of Different Tree Topologies (see Basic Protocol 3),” 
>        3rd paragraph, 1st sentence [beginning “Shimodaira and Hasegawa 
>        (1999)...”]: We reworded this text for clarity; please check 
>        to make sure that everything is correct.

OK

>    (c) 5th paragraph, beginning “KH is a pairwise test....”: We have 
>        edited the sentence starting “KH is a pairwise test......” 
>        as it was incomplete in the submitted manuscript. Please check 
>        we have retained the correct meaning and edit as necessary.

OK

> 10. Commentary, Background Information, 
>    (a) 3rd paragraph, last sentence: Please rephrase this sentence 
>        (starting “On the other hand,...”) as it does not make sense.

The sentence IMHO still says exactly what it should, but I changed
"On the other hand" to "In addition" and added a reference to the
"Suggestions for Further Analysis" where it is explained a bit. 

>    (b) 4th paragraph: What is meant by “tree-likeness”? Please explain 
>        or rephrase.

I added the definition in the "General Aspects"

> 11. Internet Resources: The URL 
>     http://rdp.cme.msu.edu/download/programs/TreeTool/ no longer appears 
>     to be valid (leads to error message from RDP webmaster). 
>     Please provide a more current address.
 
http://rdp8.cme.msu.edu/download/programs/TreeTool/