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</style></head><body><h1>Scribing Preparations</h1>
<h2>Lecture 18: Phylogenomics: Gene/species trees, reconciliation, recombination graphs</h2>
<h3>Ethan Sherbondy & Orit Giguzinsky</h3>
<h3>6.047 Fall 2012</h3>
<p>This material corresponds to Lecture 16 in the notes posted here:<br><a href="http://compbio.mit.edu/teaching.html">CompBio Teaching</a></p>
<p>This is Chapter 22 in the latest textbook draft.</p>
<h2>Scoring Matrix</h2>
I plan to write the initial draft of the missing sections at the end of the chapter.
I'll also be sweeping through the existing notes to amend typos, poor wording, and run-ons.
The diagrams on page 268 need to be broken up and placed in appropriate locations throughout the
chapter. Most diagrams also demand further explanation. After correcting the existing content, I'll
probably do another sweep through to reconsider how the notes should be organized.
<table>
<tbody><tr>
<td>Category</td>
<td>Rating</td>
<td>Justification</td>
</tr>
<tr>
<td>Structure</td>
<td>6</td>
<td>
The notes generally follow the progression of Matt's guest lecture.
Coverage of the coalescent model is poor. It is currently explained
in isolation as the legend for Figure 22.17. The topic deserves its
own proper subsection.
</td>
</tr>
<tr>
<td>Clarity</td>
<td>4</td>
<td>
The chapter is poorly written. It's riddled with grammatical errors,
and run-on sentences. Algorithm explanations in particular could do
with substantial reshaping to increase clarity. Often phrases are introduced,
e.g. gene tree, and remain unexplained until much later in the chapter.
</td>
</tr>
<tr>
<td>Completeness</td>
<td>4</td>
<td>
This chapter is currently very short. It's a little unclear why
this material isn't just part of Chapter 21, since it ends up
revisiting a lot of the same ideas (eg: paralogs v. orthologs)
without much added depth. Sections 22.8-22.11 have yet to be
written.
</td>
</tr>
<tr>
<td>Figures</td>
<td>5</td>
<td>
Figures seem to be scattered somewhat
randomly throughout the chapter. Many of them are left unexplained,
and others aren't explained until 2+ pages after they're displayed.
</td>
</tr>
<tr>
<td>Overall Quality</td>
<td>4</td>
<td>This chapter needs a ton of work to thoroughly and clearly
cover the material presented. I'd like to substantially rewrite
and expand on the notes. The figures themselves are great, but
most are left unexplained.
</td>
</tr></tbody></table></body></html>