Table 1 Definitions of the parameters and factors used in Equation (13) of the KM model
From: Accurate and fast methods to estimate the population mutation rate from error prone sequences
Parameter or factor | Description |
|---|---|
m s | The number of segregating sites within the current set of sampled and/or ancestral sequences |
σ i | Counts the number of "singletons" for sampled or ancestral sequence i. Here, "singleton" refers both to the derived mutations of the shared polymorphisms for the sampled sequences as well as to those of the observed singletons (in the strict sense) within the original dataset (Figure 3). |
P c (α i (S)) | Probability of α i (S), which is the current set of sampled and/or ancestral sequences prior to a mutation in sequence i |
P c (β ij (S)) | Probability of β ij (S), which is the current set of sampled and/or ancestral sequences after the coalescence of combinable sequences i and j (s i ~ s j ; see below) |
P c (S) | Probability of S, which is the current ordered set of n sampled and/or ancestral sequences (s1, s2, ..., s n ) during a particular coalescent interval in the genealogy |
s i , s j | Sampled and/or ancestral sequences i and j (where i ≠ j) |
s i ~ s j | Signifies that the available regions of sampled and/or ancestral sequences i and j are at least compatible and that the two are therefore combinable (i.e., can coalesce) |
|s i | | Measures the relative degree to which sampled or ancestral sequence i is a complete or partial sequence. Thus, Σ i |s i | summarizes the total available length of all sampled and/or ancestral sequences during a particular coalescent interval. |
|S| | Summarizes the current number of sampled and/or ancestral sequences during a particular coalescent interval in the genealogy |