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Dear Giancarlo
First of all, please note that you should use a distance matrix for building phylogenetic trees (whether you use UPGMA or NJ algorithms). That is, in a pairwise distance matrix an entry of 1 should refer to maximum dissimilarity (and thus minimum similarity). You may already be doing that, but it was not clear from you e-mail, so I wanted to point it out to you.
Second, when you provide a distance matrix to MEGA, it does not have the original data to generate bootstrapped datasets (i.e., resample with replacement). For this reason, you cannot generate any bootstrap values when using distance data in MEGA.
with best wishes
Sudhir Kumar |
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