From 1406a9308167d74834799e512624c0b7bc4f0767 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Sat, 12 Sep 2026 10:46:59 +0200 Subject: [PATCH] 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 | 48 ++++++++++++++++++++++++------------------------ usage-phylo.md | 48 +++++------------------------------------------- 2 files changed, 29 insertions(+), 67 deletions(-) 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: