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Update glossary.md #3340

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15 changes: 10 additions & 5 deletions docs/glossary.md
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Expand Up @@ -36,11 +36,16 @@ tree
(sec_data_model_definitions_tree_sequence)=

tree sequence
: A "succinct tree sequence" (or tree sequence, for brevity) is an efficient
encoding of a sequence of correlated trees, such as one encounters looking
at the gene trees along a genome. A tree sequence efficiently captures the
structure shared by adjacent trees, (essentially) storing only what differs
between them.
: A "succinct tree sequence" (or tree sequence, for brevity) is an object
that stores the genetic ancestry and mutational history of a set of
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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@gregorgorjanc gregorgorjanc Nov 26, 2025

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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.

is encoded by linking *nodes* (genomes) via *edges*, forming a network
or graph. Graphs of this sort are sometimes known as ancestral
recombination graphs (ARGs), so that tree sequences provide a
flexible way to encode multiple types of ARG.

(sec_data_model_definitions_node)=

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