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Reference ARGs in the glossary when defining a "tree sequence". I hope this clarifies rather than adds to any confusion.

We can address the "what is a tree sequence" stuff in the tutorials too.

Reference ARGs in the glossary
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docs/glossary.md Outdated
aligned DNA sequences. The name reflects the idea that a common
way to treat genetic ancestry is as a sequence of correlated
"trees" along the genome; a tree sequence provides an efficient
way to store differences between these trees. Technically, ancestry
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way to store differences between these trees. Technically, ancestry
way to store shared branches between these trees. Technically, ancestry

The edge table is storing what is shared, not what is different across local trees. I know this is nitpicking, but thinking in terms of differences I have read in many places really confused me when I started to read about what is tree sequence. The left-right algorithms work with differences, I believe.

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hyanwong commented Dec 3, 2025

Hi @gregorgorjanc - I have reworded slightly to take account of your point, and also added a glossary item for position. Could you have a look through the changes and check they now make sense to you? I have also put in some links between the words in the definitions, as I think that is useful.

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@hyanwong thanks for considering my nitpicking comment;) It reads very clear to me now. I have spotted one typo. Otherwise LGTM!

Co-authored-by: Gregor Gorjanc <[email protected]>
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hyanwong commented Dec 3, 2025

Excellent, thanks for spotting that (and accepted)

Co-authored-by: Jerome Kelleher <[email protected]>
@hyanwong hyanwong added this pull request to the merge queue Dec 4, 2025
Merged via the queue into tskit-dev:main with commit 9ac0b6a Dec 4, 2025
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3 participants