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Update 04-TDA-in-pangenomes.md
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nselem authored Jul 29, 2024
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In this data frame, we can see the history of the formation of families (simplices) at the different birth and death times.
If we filter at `t_death=2`we can see only the families that we remain with in the end.

> ## Exercise 1(Begginer): Partitioning the pangenome
> ## Exercise 1(Beginner): Partitioning the pangenome
> Filter the table by `t_death=2`, at this point in the filtration, which families are in each partition **Core**, **Shell** and **Cloud**?
> How many of these are single-copy core families?
> > ## Solution
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> {: .solution}
{: .challenge}

> ## Excercise 2(Begginer): Looking for functional families
> ## Excercise 2(Beginner): Looking for functional families
> In the episode [Measuring Sequence Similarity](https://carpentries-incubator.github.io/pangenomics/04-sequence_distance/index.html) we saw that the genes 2603V|GBPINHCM_01420, 515|LHMFJANI_01310, A909|MGIDGNCP_01408, and NEM316|AOGPFIKH_01528 make the
> functional family 30S ribosomal protein. Look for these genes in the `aux_simplex_list`. Are they in the same family? Are there other genes in this family?
>
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