Anyone know how to interpret the matrix of distance genetic whose analysis were performed in the software MEGA 5.0 (Tamura et al. 2011) using the pairwise method with the p-distance model?
If you multiple those values per 100 you will get the percentage of difference (0.7% and 25%).
P-distance should just be the uncorrected pairwise distance - so if it says 2% and the comparison was between 100 basepairs of sequence, that means 2 bp differ between compared samples.
Maybe someone can confirm this
Aaron is correct, the p distance is the proportion of nucleotide sites that differ between two sequences. It does not make any correction for multiple substitution, biases, etc. MEGA simply counts the number of differences between two sequences and divides it by the number of sites available for the comparison.
If your data includes any Indels these are not counted. This may be of importance if you work with non-ciding sequences (e.g. ITS or RNA).
but if the sequences are grouped: Distance, Compute between Group mean distance, p-distance,
In this case, Should it be interpreted as corrected or uncorrected?
So essentially the higher the p-distance, the more the two sequences have diverged from each other?
I used Mega and I got some values like 0.007 and 0.251. These values means the number of different sites between two sequences or the percentage of different sites? I would appreciate some help.
If you multiple those values per 100 you will get the percentage of difference (0.7% and 25%).
Thank you very much Suellen Zatti. I thought it was like this, but I was afraid to make a mistake.
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