Revised manuscript. Added manuscript in the PNAS format for revisions.

ThibaultLatrille · Jan 16, 2023 · 38b9e49 · 38b9e49
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diff --git a/manuscript/codon_models.bib b/manuscript/codon_models.bib
diff --git a/manuscript/codon_models.bib b/manuscript/codon_models.bib
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+/home/thibault/Documents/codon_models.bib
diff --git a/manuscript/compile.sh b/manuscript/compile.sh
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+latexdiff main-biorxiv.tex main-revision.tex > diff.tex
+pdftk A=reviewers-comment.pdf B=diff.pdf cat A2-11 B output reviewers-response.pdf
diff --git a/manuscript/diff.tex b/manuscript/diff.tex
diff --git a/manuscript/main-PNAS.tex b/manuscript/main-PNAS.tex
diff --git a/manuscript/main-biorxiv.tex b/manuscript/main-biorxiv.tex
@@ -418,7 +418,7 @@
 
     \begin{figure*}[htb]
         \centering
-        \includegraphics[width=0.95\linewidth, page=1]{polymorphism-method}
+        \includegraphics[width=0.95\linewidth, page=1]{figure2}
         \caption{
             Integrating divergence and polymorphism for the detection of adaptation.
             At the phylogenetic level, $\omega$ (classical codon models) and $\omega_{0}$ (mutation-selection codon models) are computed from protein-coding DNA alignments, allowing to classify genes into adaptive (in red) and nearly-neutral (in green) regime.
@@ -430,7 +430,7 @@
 
     \begin{figure*}[htb]
         \centering
-        \includegraphics[width=0.95\linewidth, page=1]{unfolded-MK}
+        \includegraphics[width=0.95\linewidth, page=1]{figure3}
         \caption{
             Enrichment of adaptation at the population-genetic scale for $29$ populations across $7$ genera at the gene (panel A) and site (panels B and C) level.
             For each population, $\rateApop$ is computed on $822$ genes (A) and $104,129$ sites (B) having a high rate of adaptation at the phylogenetic scale ($\omega > \omega_0$ in red).

diff --git a/manuscript/main-revision.tex b/manuscript/main-revision.tex