Hello. Please understand that i'm not proficient in English.
I wonder the means of "bootstrap likelihood" in RAxML.
I'm running ML+Rapid bootstrap for analysis settings, about 1428 taxa, DNA sequence, on the standard-RAxML-master using our server(NOT RAxML gui1.5b1 in WINDOW).
But I can't understand this bootstrap likelihood value.
My running situation is below
Bootstrap[0]: Time 1157.559750 seconds, bootstrap likelihood -168810.464641, best rearrangement setting 13
I wanna know that what -168810.464641 is.
In addition, what is this optimal value?? (For example, in Bayesian inference using Mrbayes, convergence diagnostic
As you probably know, when you do a ML tree search, you will get a best ML tree based on your DNA alignment, and this tree will have a certain likelihood value (that you will also get at the end of your analysis).
However, as you probably know too, for every bootstrap pseudoreplicate (usually 100 or 1000 times), the program will generate a new alignment by choosing randomly N columns (some columns will be chosen several times and others will be absent) from your original alignment of N columns.
Therefore, every time the program will do a new tree search from this new alignment (for each bootstrap pseudoreplicate), the likelihood of the subsequent tree (and potentially the tree topology itself) will be different, because the alignment on which you do the search is different from the original alignment (original alignment from which the likelihood of the best tree is calculated), and this is the value of this specific tree generated by the bootstrap search that is given to you.
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