14. Neighbor joining

[@oglala_lakota2o]

I really enjoy your videos! It helps me understand the concepts behind some of the programs and the methods they are using when I am doing analysis

[@KevinBioinformatics]

Thanks. It is indeed important to understand the methods when using programs that implement them.

[@taskinberkay]

In my notes the equation we use to find Q values is D(A,B)-(rA+rB)/(N-2)

[@KevinBioinformatics]

It is equivalent, by having all values divided by the number of clusters minus 2.

[@JJ-lo6up]

will you upload more video about bioinformatics algorithm, such as pca, umap... it's so clear for me to understand, thank you

[@KevinBioinformatics]

Yes, some more videos will be uploaded in the coming months. Stay tuned!

[@rishav513]

Here, how we calculate distance between AC and B in matrix, i don't understand

[@KevinBioinformatics]

d(AC,B) = [d(A,B) + d(C,B) - d(A,C)] / 2 = [8 + 8 - 4] / 2 = 6

[@sumto7871]

how do i know the distance between 2 hub is 1? where is the hint? the math also works when distance between hub go larger and the branches linking hub to B and D shorter

[@KevinBioinformatics]

Sorry for the late reply -- I didn't get the email notification of your comment for some reason. That distance is 1 because it is calculated by d(AC,B)/2 + [u(AC)-u(B)]/[2(3-2)] = 6/2 + [10-14]/2 = 3 - 2 = 1.

[@yatta4059]

Great video, Kevin! Hope all is well now at CUHK

[@KevinBioinformatics]

Thank you. We have been back to work.

[@AssassinDude]

Nice clear explanations and example. Thank you for this. It helped clear things up for me.

[@KevinBioinformatics]

Glad that the video was useful for you!

[@worldi86]

How did you get 6 for the distance between AC and B for the second d board ?

[@KevinBioinformatics]

It is equal to [d(A,B)+d(B,C)-d(A,C)]/2 = (8+8-4)/2 = 6

[@muhammadbabar7432]

For the second node why did you introduce a 1 between the nodes, like is there some way to find out that distance or do we always just assume that we should introduce 1 between nodes?

[@KevinBioinformatics]

Do you mean the number on the edge that connects {A,C} and {A,B,C}? It is based on the formula given on the previous page: d(AC,B)/2+[u(AC)-u(B)]/[2(r-2)] = 6/2+[10-14]/[2(3-2)] = 3-2 = 1.

[@gouthams6711]

the calculation of ur 2ed table is wrong

[@KevinBioinformatics]

Thank you for your comment. Could you explain how it is wrong?