Update sidebar separators and refine SNP model definitions

Modifies list item formatting in the sidebar to use double pipe separators. Also updates mathematical definitions and parameter sets for several SNP models, including new parameters for `snp-tn93`.

_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]]

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: