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`.
Eric Coissac committed
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@@ -1,29 +1,29 @@
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# Wiki sidebar
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# Wiki sidebar
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- [[Home|Home]]
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- [[Home\|Home]]
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- [[installation|Installation]]
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- [[installation\|Installation]]
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## Theory
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## Theory
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- [[theory-kmers_and_superkmers|Kmers and super-kmers]]
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- [[theory-kmers_and_superkmers\|Kmers and super-kmers]]
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- [[theory-encoding|DNA encoding]]
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- [[theory-encoding\|DNA encoding]]
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- [[theory-entropy_filter|Low-complexity kmer filter]]
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- [[theory-entropy_filter\|Low-complexity kmer filter]]
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- [[theory-minimizer_selection|Minimizer selection]]
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- [[theory-minimizer_selection\|Minimizer selection]]
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- [[theory-indexing_architecture|Partitioning and indexing architecture]]
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- [[theory-indexing_architecture\|Partitioning and indexing architecture]]
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## Usage
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## Usage
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- [[usage-superkmer|superkmer]]
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- [[usage-superkmer\|superkmer]]
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- [[usage-index_command|index]]
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- [[usage-index_command\|index]]
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- [[usage-merge|merge]]
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- [[usage-merge\|merge]]
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- [[usage-filter|filter]]
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- [[usage-filter\|filter]]
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- [[usage-select|select]]
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- [[usage-select\|select]]
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- [[usage-query|query]]
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- [[usage-query\|query]]
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- [[usage-dump|dump]]
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- [[usage-dump\|dump]]
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- [[usage-annotate|annotate]]
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- [[usage-annotate\|annotate]]
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- [[usage-phylo|phylo]]
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- [[usage-phylo\|phylo]]
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- [[usage-unitig|unitig]]
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- [[usage-unitig\|unitig]]
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- [[usage-estimate|estimate]]
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- [[usage-estimate\|estimate]]
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- [[usage-convert|convert]]
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- [[usage-convert\|convert]]
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- [[usage-utils|utils]]
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- [[usage-utils\|utils]]
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- [[usage-pack|pack]]
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- [[usage-pack\|pack]]
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- [[usage-predicates|Predicates and taxonomy paths]]
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- [[usage-predicates\|Predicates and taxonomy paths]]
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## Formats
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## Formats
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- [[formats-index_layout|Index construction and on-disk layout]]
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- [[formats-index_layout\|Index construction and on-disk layout]]
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- [[architecture|Architecture notes]]
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- [[architecture\|Architecture notes]]
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+5
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@@ -59,61 +59,23 @@ $$d = -\frac{3}{4}\ln\!\left(1-\frac{4p}{3}\right)$$
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**`snp-k2p`**
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**`snp-k2p`**
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$$
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$$\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}$$
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\begin{aligned}
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a_1 &= 1-2P-Q \\
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a_2 &= 1-2Q \\
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d &= -\frac{1}{2}\ln a_1-\frac{1}{4}\ln a_2
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\end{aligned}
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$$
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**`snp-k81`**
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**`snp-k81`**
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$$
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$$\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}$$
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\begin{aligned}
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a_1 &= 1-2P-2Q_1 \\
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a_2 &= 1-2P-2Q_2 \\
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a_3 &= 1-2Q_1-2Q_2 \\
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d &= -\frac{1}{4}\left(\ln a_1+\ln a_2+\ln a_3\right)
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\end{aligned}
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$$
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**`snp-f81`**
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**`snp-f81`**
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$$
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$$\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}$$
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\begin{aligned}
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E &= 1-\left(\pi_A^2+\pi_C^2+\pi_G^2+\pi_T^2\right) \\
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d &= -E\ln\!\left(1-\frac{p}{E}\right)
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\end{aligned}
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$$
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**`snp-t92`**
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**`snp-t92`**
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$$
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$$\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}$$
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\begin{aligned}
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g &= \pi_C+\pi_G \\
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w &= 2g(1-g) \\
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a_1 &= 1-\frac{P}{w}-Q \\
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a_2 &= 1-2Q \\
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d &= -w\ln a_1-\frac{1}{2}(1-w)\ln a_2
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\end{aligned}
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$$
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**`snp-tn93`**
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**`snp-tn93`**
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$$
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$$\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}$$
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\begin{aligned}
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g_R &= \pi_A+\pi_G \\
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g_Y &= \pi_C+\pi_T \\
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k_1 &= \frac{2\pi_A\pi_G}{g_R} \\
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k_2 &= \frac{2\pi_C\pi_T}{g_Y} \\
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k_3 &= 2\left(g_Rg_Y-\frac{\pi_A\pi_G\,g_Y}{g_R}-\frac{\pi_C\pi_T\,g_R}{g_Y}\right) \\
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w_1 &= 1-\frac{P_1}{k_1}-\frac{Q}{2g_R} \\
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w_2 &= 1-\frac{P_2}{k_2}-\frac{Q}{2g_Y} \\
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w_3 &= 1-\frac{Q}{2g_Rg_Y} \\
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d &= -k_1\ln w_1-k_2\ln w_2-k_3\ln w_3
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\end{aligned}
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$$
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**`snp-tv`** — transversions only, deliberately uncorrected:
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**`snp-tv`** — transversions only, deliberately uncorrected:
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