Neighbor Joining Fitsch Margoliash - PowerPoint PPT Presentation
1 / 7
Title:
Neighbor Joining Fitsch Margoliash
Description:
Find branch lengths between i and j by treating remaining sequences as composite ... I and II are closest neighbors at distance 10. Question: Which of them is closer ... – PowerPoint PPT presentation
Number of Views:117
Avg rating:3.0/5.0
Title: Neighbor Joining Fitsch Margoliash
1
Neighbor Joining (Fitsch Margoliash)
- Generates unrooted tree, allowing for unequal
branches - Given Distance matrix for sequences
- Steps Repeat 1-3 till all branches generated
- Take any two sequences i, j
- Find branch lengths between i and j by treating
remaining sequences as composite (c) - Calculate average i-C and j-C distances
- Calculate branch lengths i and j
- Treat ij as composite sequence now and generate
new distance table. - Generate multiple trees by starting with
different pairs - Compare resulting trees in terms of best fit to
original distance matrix
2
(No Transcript)
3
- I and II are closest neighbors at distance 10.
Question Which of them is closer to the rest,
and by how much? - Average distance from I to III, IV 40
- Average distance from II to III, IV 45
- X Z 40
- Y Z 45 gt x 2.5 y 7.5
- X Y 10
x
z
I
II
y
4
- Established
- Now, consider (I,II) as composite sequence and
find closest pairs - For 4 sequences, trivial that III,IV should be
the closest (Why?)
2.5
I
II
7.5
5
III
A
2.5
C
I
II
B
7.5
IV
- A B 20
- 2.5 C A 30 ?
- 7.5 C B 50
A 2.5 B 17.5 C 25
6
Predicted Tree
III
2.5
2.5
25
I
7.5
17.5
II
IV
7
Predicted Distance matrix
Error (52 52 52)1/2 8.66 Repeat
entire process starting with a different
pair Tree with lowest error is the best one
Recommended
CrystalGraphics Presentations
![[PDF] READ Free My Neighbor Totoro Sketchbook PowerPoint PPT Presentation](https://s3.amazonaws.com/images.powershow.com/10070523.th0.jpg?_=20240702050)
