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Estimation was performed using restricted maximum likelihood (option —reml).
General practice was fitted as a random effect using the 'xtreg' command in Stata with the maximum likelihood option [ 21].
All genetic parameters were computed by the Qxpak program with the REML (restricted maximum likelihood) option [ 10].
We explored the contribution of these variables to heterogeneity by meta-regression using the "metareg" command in Stata (version 9.2) software with the restricted maximum likelihood option.
This matrix, containing every SNP in the data set, was used in the dnadist algorithm of PHYLIP using the maximum likelihood option.
Using the appropriate model (GTR+I+Γ) we conducted heuristic searches with 100 random starting addition sequences using maximum likelihood option in PAUP*.
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We selected the maximum-likelihood option and three runs of medium length in Colony for all N e estimates.
The analysis was conducted using the variance component analysis procedure, Residual Maximum Likelihood (REML) option, in Genstat [16].
The selected sequences were then each processed against all ss-rRNA sequences by two methods: by using STAP with the default maximum likelihood tree option selected, and by using BLASTN.
The number of maximum linkages to show per locus was set to 0. As algorithm we used the ML (Maximum Likelihood) mapping option, and within the map building, the spatial sampling thresholds were set one to 0.1 the first and the rest to 0. The 'Number of map optimization rounds per sample' was fixed to 1.
A neighbor-joining tree was conducted in MEGA 4 [ 74] using the complete deletion of ambiguous data and the maximum composite likelihood option.
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