Outgroup bacterial 16S sequences were obtained from GenBank and included in the alignment with the endosymbiont data (Table 4).
In the first step, PM data was used to guide model refinement, which involved the manual addition and removal of reactions to bring it into better alignment with the PM data.
Exome sequence analysis can be generally summarized as a two step process with alignment of the data to a human genome reference followed by subsequent genetic variant calling from the post-alignment data, or, more simply, the identification of specific sequence alterations that are polymorphisms, rare variants or mutations.
Then, a multiple-sequence alignment was performed with the data set with BioNumerics software for windows (version 5.1, Applied Maths).
The phasing model is learnt using an analysis-synthesis loop that iterates HMM estimations and forced alignments with the original data.
Functional data were placed on the cortical surface by first registering structural images obtained during the experiment, which were already in alignment with functional data, with the high-resolution structural images used to create the cortical surfaces (3dvolreg in AFNI).
Deduced amino acid sequence alignments were performed with the data for each isolates of CHY topotype using SeqMan II.
The total number of sequences that remained after applying all of the filtering rules and that were used for alignment with the reference genome for Data 12, Data15, and Data 20 are shown in Table 1. a Mean (s.e).e
The per-site likelihoods of the 16S topology and the topology based on the butyrate kinase alignment were calculated using FastTree with the butyrate kinase alignment as the data set, and an approximately unbiased (AU) test was performed using CONSEL (Shimodaira and Hasegawa 2001).
We show that robustness against filtering, agreement with a maximum likelihood function that takes into account experimental artifacts, the Kuiper statistic test, and alignment with synthetic data all identify the Weibull or stretched exponential distribution as the best fitting model.
