diff --git a/_Sidebar.md b/_Sidebar.md
index cc19287..11e6539 100644
--- a/_Sidebar.md
+++ b/_Sidebar.md
@@ -1,29 +1,29 @@
 # Wiki sidebar
 
-- [[Home|Home]]
-- [[installation|Installation]]
+- [[Home\|Home]]
+- [[installation\|Installation]]
 ## Theory
-  - [[theory-kmers_and_superkmers|Kmers and super-kmers]]
-  - [[theory-encoding|DNA encoding]]
-  - [[theory-entropy_filter|Low-complexity kmer filter]]
-  - [[theory-minimizer_selection|Minimizer selection]]
-  - [[theory-indexing_architecture|Partitioning and indexing architecture]]
+  - [[theory-kmers_and_superkmers\|Kmers and super-kmers]]
+  - [[theory-encoding\|DNA encoding]]
+  - [[theory-entropy_filter\|Low-complexity kmer filter]]
+  - [[theory-minimizer_selection\|Minimizer selection]]
+  - [[theory-indexing_architecture\|Partitioning and indexing architecture]]
 ## Usage
-  - [[usage-superkmer|superkmer]]
-  - [[usage-index_command|index]]
-  - [[usage-merge|merge]]
-  - [[usage-filter|filter]]
-  - [[usage-select|select]]
-  - [[usage-query|query]]
-  - [[usage-dump|dump]]
-  - [[usage-annotate|annotate]]
-  - [[usage-phylo|phylo]]
-  - [[usage-unitig|unitig]]
-  - [[usage-estimate|estimate]]
-  - [[usage-convert|convert]]
-  - [[usage-utils|utils]]
-  - [[usage-pack|pack]]
-  - [[usage-predicates|Predicates and taxonomy paths]]
+  - [[usage-superkmer\|superkmer]]
+  - [[usage-index_command\|index]]
+  - [[usage-merge\|merge]]
+  - [[usage-filter\|filter]]
+  - [[usage-select\|select]]
+  - [[usage-query\|query]]
+  - [[usage-dump\|dump]]
+  - [[usage-annotate\|annotate]]
+  - [[usage-phylo\|phylo]]
+  - [[usage-unitig\|unitig]]
+  - [[usage-estimate\|estimate]]
+  - [[usage-convert\|convert]]
+  - [[usage-utils\|utils]]
+  - [[usage-pack\|pack]]
+  - [[usage-predicates\|Predicates and taxonomy paths]]
 ## Formats
-  - [[formats-index_layout|Index construction and on-disk layout]]
-- [[architecture|Architecture notes]]
+  - [[formats-index_layout\|Index construction and on-disk layout]]
+- [[architecture\|Architecture notes]]
diff --git a/usage-phylo.md b/usage-phylo.md
index db40e84..67fbdcd 100644
--- a/usage-phylo.md
+++ b/usage-phylo.md
@@ -59,61 +59,23 @@ $$d = -\frac{3}{4}\ln\!\left(1-\frac{4p}{3}\right)$$
 
 **`snp-k2p`**
 
-$$
-\begin{aligned}
-a_1 &= 1-2P-Q \\
-a_2 &= 1-2Q \\
-d   &= -\frac{1}{2}\ln a_1-\frac{1}{4}\ln a_2
-\end{aligned}
-$$
+$$\begin{aligned} a_1 &= 1-2P-Q \\ a_2 &= 1-2Q \\ d   &= -\frac{1}{2}\ln a_1-\frac{1}{4}\ln a_2 \end{aligned}$$
 
 **`snp-k81`**
 
-$$
-\begin{aligned}
-a_1 &= 1-2P-2Q_1 \\
-a_2 &= 1-2P-2Q_2 \\
-a_3 &= 1-2Q_1-2Q_2 \\
-d   &= -\frac{1}{4}\left(\ln a_1+\ln a_2+\ln a_3\right)
-\end{aligned}
-$$
+$$\begin{aligned} a_1 &= 1-2P-2Q_1 \\ a_2 &= 1-2P-2Q_2 \\ a_3 &= 1-2Q_1-2Q_2 \\ d   &= -\frac{1}{4}\left(\ln a_1+\ln a_2+\ln a_3\right) \end{aligned}$$
 
 **`snp-f81`**
 
-$$
-\begin{aligned}
-E &= 1-\left(\pi_A^2+\pi_C^2+\pi_G^2+\pi_T^2\right) \\
-d &= -E\ln\!\left(1-\frac{p}{E}\right)
-\end{aligned}
-$$
+$$\begin{aligned} E &= 1-\left(\pi_A^2+\pi_C^2+\pi_G^2+\pi_T^2\right) \\ d &= -E\ln\!\left(1-\frac{p}{E}\right) \end{aligned}$$
 
 **`snp-t92`**
 
-$$
-\begin{aligned}
-g   &= \pi_C+\pi_G \\
-w   &= 2g(1-g) \\
-a_1 &= 1-\frac{P}{w}-Q \\
-a_2 &= 1-2Q \\
-d   &= -w\ln a_1-\frac{1}{2}(1-w)\ln a_2
-\end{aligned}
-$$
+$$\begin{aligned} g   &= \pi_C+\pi_G \\ w   &= 2g(1-g) \\ a_1 &= 1-\frac{P}{w}-Q \\ a_2 &= 1-2Q \\ d   &= -w\ln a_1-\frac{1}{2}(1-w)\ln a_2 \end{aligned}$$
 
 **`snp-tn93`**
 
-$$
-\begin{aligned}
-g_R &= \pi_A+\pi_G \\
-g_Y &= \pi_C+\pi_T \\
-k_1 &= \frac{2\pi_A\pi_G}{g_R} \\
-k_2 &= \frac{2\pi_C\pi_T}{g_Y} \\
-k_3 &= 2\left(g_Rg_Y-\frac{\pi_A\pi_G\,g_Y}{g_R}-\frac{\pi_C\pi_T\,g_R}{g_Y}\right) \\
-w_1 &= 1-\frac{P_1}{k_1}-\frac{Q}{2g_R} \\
-w_2 &= 1-\frac{P_2}{k_2}-\frac{Q}{2g_Y} \\
-w_3 &= 1-\frac{Q}{2g_Rg_Y} \\
-d   &= -k_1\ln w_1-k_2\ln w_2-k_3\ln w_3
-\end{aligned}
-$$
+$$\begin{aligned} g_R &= \pi_A+\pi_G \\ g_Y &= \pi_C+\pi_T \\ k_1 &= \frac{2\pi_A\pi_G}{g_R} \\ k_2 &= \frac{2\pi_C\pi_T}{g_Y} \\ k_3 &= 2\left(g_Rg_Y-\frac{\pi_A\pi_G\,g_Y}{g_R}-\frac{\pi_C\pi_T\,g_R}{g_Y}\right) \\ w_1 &= 1-\frac{P_1}{k_1}-\frac{Q}{2g_R} \\ w_2 &= 1-\frac{P_2}{k_2}-\frac{Q}{2g_Y} \\ w_3 &= 1-\frac{Q}{2g_Rg_Y} \\ d   &= -k_1\ln w_1-k_2\ln w_2-k_3\ln w_3 \end{aligned}$$
 
 **`snp-tv`** — transversions only, deliberately uncorrected: