MultiRS07 — Redelings & Suchard (2007) model of
insertions and deletions.
Usage
MultiRS07(f1: Double, rate: Double, logRatio: Double, meanLength: Double, topology: Topology) → IndelModel
Arguments
A default beginning with ~ specifies a prior
distribution.
-
f1: -
The fraction of sites with the lower rate
-
Default:
~Beta(1,2) -
rate: -
The insertion-deletion rate
-
Default:
~LogLaplace(-4,0.707) -
logRatio: -
The log-ratio between the two rates
-
Default:
~Exponential(0.1) -
meanLength: -
The mean indel length
-
Default:
~ShiftedExponential(10,1) -
topology -
Default: The topology in the current context
Original default expressions
-
topology -
get_state(topology)
Description
This model allows insertion and deletions (indels) of multiple
residues. Indel lengths are geometrically distributed. Insertions and
deletions are symmetric in this model.
Note that the insertion-deletion rate is normalized to the substitution
rate, so that if rate=1.0, then the insertion-deletion rate is the same
as the substitution rate.
Note that the mean indel length must be at least 1.
Citation
Redelings, Benjamin D; Suchard, Marc A (2007). Incorporating indel information into phylogeny estimation for rapidly emerging pathogens.. BMC Evolutionary Biology 7(1): 40. DOI: 10.1186/1471-2148-7-40