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-This is a page containing some information about the project.
+# tfpbrowser
+
+## About
+
+The Transmission Fitness Polymorphism Browser (tfpbrowser) is a visualisation tool for output from
+the Transmission Fitness Polymorphism Scanner (tfpscanner)[1-3]. Information on the visualisation
+options can be found below, while details regarding installation of the tfpbrowser package and the
+source code can be found at
+[https://github.com/mrc-ide/tfpbrowser](https://github.com/mrc-ide/tfpbrowser).
+
+Six different visualisations can be accessed by selecting from the ‘View’ dropdown menu on the
+left-hand side. If the ‘View’ option is not visible, then the left-hand side menu may need to be
+expanded by clicking on the double arrow button.
+
+### Tree Visualisations
+
+There are four different tree visualisation options. These are described below, but a number of
+characteristics are common to each tree visualisation:
+
+- The size of the circles (for internal nodes) and triangles (tips) indicates the size of the
+cluster that they represent.
+- The colour indicates a particular characteristic of the cluster.
+- On the right-hand side of each tree visualisation, the colouring of the bars indicates whether a
+genotype (for which a key mutation is labelled) is present (true) or absent (false) in the clusters
+at the same vertical level.
+- Further information on each cluster can be viewed by hovering over it with the mouse cursor.
+
+The four tree visualisation options in the ‘View’ menu are:
+
+#### Tree Clock Outlier
+
+Displays a phylogenetic tree with clusters colour coded (key at the top) according to the value of
+the molecular clock outlier (MCO) statistic. This is computed by the tfpscanner as a measure of the
+degree to which evolutionary rates differed in the lineage leading to a phylogenetic cluster.
+Root-to-tip regression is used to predict the divergence of tips in a cluster and contrasts this
+with divergence within an ancestral clade including the given cluster. This predicted divergence is
+then compared to the true divergence of the cluster.
+
+#### Tree Logistic Growth Rate
+
+Displays a phylogenetic tree with clusters colour coded (key at the top) according to the value of
+the logistic growth rate. This is computed in the tfpscanner using one of two different methods
+depending on the level of model support calculated using the Akaike Information Criterion (AIC) and
+‘relative likelihood’. The first method uses a generalised linear model (GLM) to calculate the log
+odds of a sample being from a cluster of interest compared to a geographically and temporally
+matched sample weighted by prevalence, and multiplied by the estimated mean generation time to
+calculate the relative LGR per generation for each cluster of interest. The second method uses a
+generalised additive model (GAM) combined with a Gaussian process model to identify changes in
+growth rates over time.
+
+#### Tree Mutations
+
+This visualisation has a ‘Mutation’ menu from which to select a particular mutation to be
+highlighted in the phylogenetic tree. Clusters containing the mutation selected will be coloured red
+in the phylogenetic tree while clusters not containing this mutation will be grey.
+
+#### Tree Sequences
+
+This visualisation has a ‘Sequence’ menu from which to select a particular sequence ID. Clusters
+containing this sequence will be coloured red in the phylogenetic tree while those not containing it
+will be grey.
+
+### Scatter plots
+
+The molecular clock outlier and logistic growth rate statistics can also be viewed in scatter plots:
+
+#### Sina Clock Outlier
+
+Displays a scatter plot of the molecular clock outlier statistic value for each phylogenetic cluster
+on the y-axis and the lineage and/or mutation is stratified along the x-axis. The plot marker
+colours indicate the lineage and/or mutation and the size indicates the cluster size, both as per
+the legend on the right-hand side of the plot. _See ‘Tree Clock Outlier’ above for details of the
+molecular clock outlier statistic_.
+
+#### Sina Logistic Growth Rate
+
+Displays a scatter plot of the logistic growth rate value for each phylogenetic cluster on the
+y-axis and the lineage and/or mutation is stratified along the x-axis. The circle colours indicate
+the lineage and/or mutation and the size indicates the cluster size, both as per the legend on the
+right-hand side of the plot. _See ‘Tree Logistic Growth Rate’ above for details of this statistic_.
+
+### Downloads
+
+Tables, plots and .rds files can also be downloaded by clicking on the ‘Cluster statistics’ tab and
+selecting the relevant option.
+
+### References
+
+[1] Volz EM, Boyd O. Transmission Fitness Polymorphism Scanner. Available from:
+https://github.com/mrc-ide/tfpscanner
+
+[2] Volz EM. Fitness, growth and transmissibility of SARS-CoV-2 genetic variants. Nat Rev Genet
+2023. https://doi.org/10.1038/s41576-023-00610-z
+
+[3] Drake KO, Boyd O, Franceschi VB, Colquhoun RM, Ellaby NAF, Volz EM. Phylogenomic early warning
+signals for SARS-CoV-2 epidemic waves. eBioMedicine 2024: 100.
+https://doi.org/10.1016/j.ebiom.2023.104939