Question: A comparison of 'Closest-neighbour-interchange' and 'Nearest-neighbour-interchnage' algorithms
gravatar for mdsiddra
6 months ago by
mdsiddra20 wrote:

I have been using different tools for reconstrucing a phylogenetic tree from data file. The tools provide different searching algorithms to be chosen for searching the best tree from data file. 'Closest-neighbour-interchange' (CNI) and 'Nearest-neighbour-interchnage' (NNI) are among those.

I want to understand, what makes the two algorithms, 'Closest-neighbour-interchange' and 'Nearest-neighbour-interchnage' different from each other?? How do the two search differently? What is the preference of chosing any of the algorithm??

It would also be helpful if I can get comparative/ or any literature data for this.

algorithm • 191 views
ADD COMMENTlink modified 6 months ago by h.mon24k • written 6 months ago by mdsiddra20

On the face of it, given that closest is synonym to nearest, the two algorithms should be the same. However, there may be implementation details that make the tools work differently. The question can't be answered without you indicating which tools you are using or pointing to a description of the two algorithms and their implementation.

ADD REPLYlink written 6 months ago by Jean-Karim Heriche18k

Oh sorry for that, I forgot to mention that I was talking about MEGA software. And I think I have found my answer in suggestions by other.

Thankyou for your helpful response.

ADD REPLYlink modified 6 months ago • written 6 months ago by mdsiddra20
gravatar for h.mon
6 months ago by
h.mon24k wrote:

I am not 100% sure, but I think some old version of MEGA used 'Closest-neighbour-interchange'. You won't find this nowadays, the name of the algorithm is 'Nearest-neighbour-interchnage', MEGA used 'Closest-neighbour-interchange' as synonymous to 'Nearest-neighbour-interchnage', but changed to 'Nearest-neighbour-interchnage' in more recent versions.

ADD COMMENTlink written 6 months ago by h.mon24k

Yes , I guess this is right, I have compared the MEGA older and newer versions and I have found the same you have suggested. Thankyou for this helpful guidance.

ADD REPLYlink written 6 months ago by mdsiddra20
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