We tally the results in this manner so as to perform a more reasonable comparison between the core alignment aspects in the context of the whole human genome of other methods.
Sequences closely related to those already present in the core alignment have been merged to the alignment manually in the BioEdit environment.
Mutation and recombination events were assigned to specific branches of the core phylogeny, and the number of recombination events affecting each site in the core alignment was calculated.
Mugsy also identified a slightly longer core alignment.
Despite differences in the alignment, the phylogenetic trees based on the two core alignments produced identical topologies with similar Bayesian support values.
"We are partnering with Silver Lake because of their incredible track record as technology investors, their understanding of digital platform businesses like ours and because of the alignment in core values we share," said Heather J. Brunner, Chairwoman and CEO of WP Engine, in a statement.
A core-alignment was also extracted by keeping regions where the 53 genomes aligned over at least 500 bp (corresponding of ~97% of the C. trachomatis chromosome), and aligned segments were concatenated into a single-core genome alignment to be further used in the construction of the species phylogenetic tree.
The high thermal conductivity results from the excellent nanotube alignment in the core of the polymer fiber and the use of liquid crystal polybenzimidazole as a matrix and shell polymer.
Running this algorithm on the E. faecium core genome alignment resulted in the prediction of 1.2 Mb of recombinant sequence, divided over 383 recombination events (supplementary fig. S3, Supplementary Material online).
Of the original 1,223,137 positions in the core genome alignment, 534,961 (44%) were predicted to be affected by recombination in at least one strain.
Actually, we used a relaxed criterion for syntenic conservation (CONS_RATIO < 1) in our core genome alignment procedure.
