Hi all,
I just started using the program TREE-PUZZLE to construct phylogenetic trees. I having the darnedest time trying to figure out how to interpret the branch lengths of the tree though. The data I feed TREE-PUZZLE are binary states (0 or 1) for roughly a million different characteristics for 8 individuals, and the branch lengths it spits out are on the order of .01. My best guess is that this number indicates that over that distance on the tree .01 of all the characters have changed. Please let me know if my question is unclear, and thanks in advance for any advice.
1 answer
Hey Fenix,
Checking out the TREE-PUZZLE manual, it seems it uses a nucleotide substitution model (F81) for what they call 'two-state' data. So, the branch lengths will be of the normal likelihood sort - expected number of substitutions per site (or changes of character-state per datum in your case)
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