If the genomes were more similar, there would not be sufficient consistent and compensatory mutations observed to infer the presence of base-pairing; if the genomes were less similar, there would not be a good enough alignment to infer structure.
Reyes and Tanaka (2010) used an infinite alleles model to define a relative rate and then benchmarked this rate against estimates of the IS6110 mutation rate to infer a MIRU mutation rate (7.00 × 10-4 1.50 × 10-2).
To explore the extent to which the idealized SBD model assuming infinitesimal mutations is able to infer fitness when evolution happens via discrete mutations, we simulated a simple model of evolution with fixed fitness variance (σ = 0.03 ) (Zanini and Neher, 2012).
In order to identify somatic mutations, it is necessary to infer the germline (pre-mutation) state for each observed sequence.
The software implements a Bayesian method based on the observed linkage disequilibrium between a disease mutation and linked markers to infer the age of the mutation (Reeve and Rannala, 2002; Rannala and Reeve, 2003).
We further estimated the population mutation parameter, θ, which in conjunction with the average mtDNA mutation rate was used to infer the effective population sizes of the different Chad Basin populations assuming a neutral model of molecular evolution (Table 4).
Therefore, accurate estimation of the MIRU mutation rate is essential to infer the relationship between transmitted strains based on typing profile.
To make a more complete cross-species comparison, we have also implemented a nonequilibrium version of the multiallele model (see Materials and Methods) in order to infer mutation rates in A. thaliana.
We go on to demonstrate the practicality of the new sampler by using it to infer mutation rates, effective population sizes and the structured tree from geographically annotated HA gene sequences derived from the Influenza A subtype H3N2 strain.
