📗 -> 03/04/25: ECS124-L14
[Lecture Slide Link]
🎤 Vocab
❗ Unit and Larger Context
Small summary
✒️ -> Scratch Notes
- Phylogenetic tree -> species evolution
- General clustering
Biological Trees
Given a distance matrix, is it additive?
How to get the distance matrix? Distance between human and mouse?
- You can additive tree
nearest neighbor (proved 1987)
Four point test for additive matrix
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- Check that the latter value are equal to each other, and that the leq statement holds true. If that is true, then the matrix is additive
Pair top with bottom - P1:
- P2:
D(A,B) D(B,C)
D(A,B) D(B,D)
D(A,D) D(C,D)
| A(j) | B(l) | C(i) | D(k) | |
|---|---|---|---|---|
| A | 18 | 3 | 17 | |
| B | 19 | 5 | ||
| C | 18 | |||
| D |
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Molecular Clock Theory
- Mutations are rare, AND occur at the same rate
- Single origin
Time zero is the time of mutation.
Ultrametric tree: Distance/height is time
- Can be created using UPGMA algo
Also, even if data not ultrametric => Create ultrametric tree
Distance matrix is ultrametric? 3-pt test
- In a set of three, one is smaller and the other two are the same if the data is ultrametric
Jukes Cantor Distance Matrix
All distance matrix come from alignment
JC69 - Markov chain model for DNA sequences
- The state of an event only depends on the state immediately preceding it (t-1 / prev)
| A | T | C | G | |
|---|---|---|---|---|
| A | ||||
| T | ||||
| C | ||||
| G | ||||
- Tends to be small
- No Mutation
…
Distance Between Two Sequences
- percentage dif
s1 = ATCCATCG
s2 = ATTCATGG
pt = 2/8
- 6 matches, 2 different, out of six
🧪 -> Refresh the Info
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🔗 -> Links
Resources
- Put useful links here
Connections
- Link all related words