Add forward refs to FP section

[jeromekelleher]

• Intro dicussion about X lineages. We're basically now saying that we don't think a bunch of things are recombinants, since they descend from Table 3C. right?
• Backbone phylo section. We want to ref forward here, saying these recombs are likely examples of what we see there

[jeromekelleher]

We focus here on the 749 Nextclade-designated recombinant samples, all but two of which descend from a recombination node in the Long ARG.

[jeromekelleher]

The most recent recombination node for 79 samples (XN: 53, XZ: 16, XAJ: 6, XE:1, XAD: 1, XAH: 1, XAK: 1) is the same.

[hyanwong]

I see Sally suggested deleting the entire para. We need to say something about the exclusion, however. How about:

79 samples (XN: 53, XZ: 16, XAJ: 6, XE:1, XAD: 1, XAH: 1, XAK: 1) trace back to a most recent recombination node that we suspect to be a false positive (row C in Table~\ref{tab:false_positives}, see Section~\ref{sec:false_positives}). For simplicity we exclude these samples from further analyses in this section.

[jeromekelleher]

Something like that. Can we keep "we" as meaning "us and the reader" rather than "we the authors" though. So rather than "we suspect", "are likely" or "may be"

[hyanwong]

Ah yes, a good distinction. I guess "we" make this passive then:

79 samples (XN: 53, XZ: 16, XAJ: 6, XE:1, XAD: 1, XAH: 1, XAK: 1) trace back to a most recent recombination node that is likely to be a false positive (row C in Table~\ref{tab:false_positives}, see Section~\ref{sec:false_positives}). For simplicity these samples are excluded from further analyses in this section.

[hyanwong]

Done