Table 1.
Summary of Notations
|
L1,L2 |
lengths of two orthologous timer sequences |
| Δ = L1-L2 | difference of lengths of timer sequences |
| δ | length of an individual indel |
| I | fraction of insertions among all indels |
| A | fraction of indels which occurred in the first of the two lineages |
| a | probability that an indel increases Δ |
| p(δ) | distribution of δ of all indels |
| Pi(δ), Pd(δ) | distributions of length of insertions and of deletions |
| p+(δ), p-(-δ) | distributions of indels with only positive and only negative values of δ |
| pm(δ), ph(δ) | distribution of indel length in muroids and in primates |
| k | number of indels on the path between two timer sequences |
| fk(Δ) | distribution of Δ between two timer sequences with a certain k |
| T | number of generations of independent evolution of timer sequences |
| b | per nucleotide site per generation probability of an indel fixation |
| q = bT | average per site number of accumulated indels |
| u(k) | probability of a timer of length L accumulating k indels, under a given q |
| Ii(q) | likelihood function for the i-th timer sequence |
| I(q) | likelihood function for a set of timer sequences |
| q^
|
maximal likelihood estimate of q
|
