In the past week there's been a spike in attention, especially due to the anniversary coinciding with the final, inexorable march to 4,000 — but for one very specified branch of the media these are the headlines that matter every day and with every number: The military media.
The 54 bp region where positive selection was detected was further analyzed using the CodeML software of the PAML package for estimating d N / d S ratios of 60 specified branches in the predefined phylogenetic tree.
The test compares a model that assumes positive selection on one branch or on a set of a priori specified branches (hypothesis H1) with a null model that does not incorporate positive selection (hypothesis H0).
More complex models assume an independent ratio for each lineage (free-ratios), variable ratios for specific classes of sequence sites (site-specific), or variable ratios for specific classes of sequence sites along specified branches (branch-site specific) [ 53- 57].
However, as we shall see in the following, it turns out that the idea of a specified branch at every moment can be integrated into the semantics in several ways.
Furthermore, with stochastic mutational mapping we did not have to pre-specify branches with potentially positively-selected sites, which is a requirement of the branch-site models in PAML.
But first of all some comments on the very idea of a specified branch.
The branch-site models A and B were used to detect positive selection in a subset of sites in a specified branch.
What makes the specified branch privileged?
Pruning branches were identified in the reconstructed trees using a simplified two-step pruning rule; (i) maintain specified branch spacing and (ii) maintain specified branch length.
The method joins a host of existing tests to detect selection sweeps along pre-specified branches of a phylogeny [ 10, 11, 31, 33, 35- 40, 42, 43].
