To control the observed substitution rates for background nucleotide composition (see Methods), the nucleotide content was determined for all known human intronic sites and FFD sites of coding regions (Table 2).
The evolutionary distances were computed using the Maximum Composite Likelihood method for the nucleotide sequences and the Jones-Taylor-Thornton (JTT) matrix-based method for the amino acid sequences.
In method 3, the nucleotide variants that were observed only once among the isolates were excluded.
We applied the support weighting method to the nucleotide data matrix.
The Kimura-2-parameter model of molecular evolution was used in the NJ method of the nucleotide sequences.
In method 1, the nucleotide difference (3.2) among five Singaporean sequences was used to adjust the sequence errors and mutations that occurred during cell culture.
The inputs for each method were the nucleotide sequence alignments of the concatenated variable nucleotide positions for the core genome among all isolates, prepared using Nesoni as described earlier and managed with SeaView v4.3.3 (Gouy et al. 2010).
Maximum likelihood was used as the tree reconstruction method, with the nucleotide substitution model (GTR), gamma rates parameter α, proportion of invariable sites and nucleotide frequencies determined using MODELTEST [ 29].
Method 2: In this method, the accession nucleotide accessions in the Chicken.na28.annot.csv file were collected and sequences used to find the best chicken Refseq nucleotide.
