Hi Kevin,
You are referring to the alignment from section 3.10 in Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
, namely Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
right?
For this alignment, the key is to include
rate variation in the analysis set up (see the attached screen shot). Without rate variation, the boundaries between more/less variable stretches of the gene can be identified as recombination breakpoints. If you use rate variation, the results are mostly congruent with the book chapter (Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
). We've revised the algorithm and HyPhy optimization routines a bit since the book was published, and since the procedure is also stochastic, some 'wobble' in the location of inferred breakpoints is expected (but look at the confidence intervals as well). Notice that the new GARD output includes breakpoint-by-breakpoint phylogenetic incongruence evaluation.
As for the influenza example, the fact that GARD infers breakpoints, could point to heterotachy or other process which generate discordant phylogenetic signal but are not recombination events. I think all the book says is that intra-gene recombination is thought to be rare in Influenza, but
Sorry for the confusion.
Sergei