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I have been working on nucleotide and protein data to reconstruct maximum parsimony trees using MEGA software to get parsimony tree, via "random addition" method is used to generate the initial tree(s).

I need to know that when randomly chosen sequences are added to reconstruct an initial tree, on what basis the best tree is chosen??

I would appreciate if anyone can guide me about this method or suggest me some good literature about this in order to make me understand the concept of this method.

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  • $\begingroup$ Is there something wrong with question? $\endgroup$
    – Sidra Younas
    Sep 19, 2018 at 2:10
  • $\begingroup$ Nothing is wrong with this question, but people do this on their own time and are not working to solve other's problems, and some might not be on the same time-zone as you. Did you try reading the original article ? $\endgroup$
    – llrs
    Sep 19, 2018 at 7:19
  • $\begingroup$ Yes, I have gone through it but it did'nt help me solving my question. $\endgroup$
    – Sidra Younas
    Sep 25, 2018 at 1:18

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MEGA manual may help to explain the criteria used in selecting the final maximum parsimony tree.

The random tree additions refers to the generation of random initial trees for a heuristic search to find MP trees. In this case, a tree is generated by randomly selecting a sequence and adding it to the growing tree on a randomly-selected branch.

Instead of using the random tree additions you can use the min-mini algorithm for the initial tree set.

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  • $\begingroup$ Thankyou for the response, but the thing is that I need to understand how can an initial tree be constructed to be used for heuristic searches to find parsimonious tree? $\endgroup$
    – Sidra Younas
    Oct 7, 2018 at 12:45

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