The iterative maximum likelihood algorithm described in [8, 11, 12] is very effective, but computationally expensive making it difficult to implement for high datarate systems.
Unsupervised hierarchical clustering of individuals based on SNP genotyping data was performed using the maximum likelihood method described in [21] which is implemented via an Expectation-Maximization algorithm in the program frappe.
The heterogeneity in the frequencies between the NFS and SFS populations was determined using the maximum likelihood procedure described in González et al. [ 15].
We applied the approximate Maximum Likelihood method described above to the values of S, η 1 and h returned by each simulation.
For each dataset, we then applied the approximate Maximum Likelihood algorithm described above, and calculated 95% confidence intervals for N A, N 0, and τ.
For this purpose, we performed the "admixture maximum likelihood" test described by Tyrer et al. [ 41] to obtain a global P-value for 165 unique SNPs from 15 cancer-related pathways (hsa052*) curated in the KEGG database.
The PBP-βL domain of thirty-seven metazoan LACTB family proteins, four Dictyostelium LACTB homologs, and ten bacterial LPBP-B proteins were aligned and analyzed by maximum likelihood as described in Methods.
A second computer program for the Phase 2 of the study was also run using Microsoft Excel to estimate the cured fraction C by using a maximum likelihood method described by Boag [ 4].
In this case D denotes the between-city variance in the effects estimates and can be estimated from the data using the maximum likelihood method described by Berkey et al. (1995).
Maximum likelihood methods described elsewhere [ 30, 31] were used to estimate the log likelihoods of models assuming either dependency or non-dependency of gene phylogeny with the discrete variation of gene traits (i.e. overlapping or non-overlapping localization in the respective genomes).
