We are working on barcoding of some spices.Sequences for rbcL locus has been generated for Piper nigrum. I would like to know how the distance is calculated?
That's quite easy:
In Mega (5.2) press Distance: Compute pairwise distances
Load your (e.g. Fasta or Mega) sequence file
In box Analysis Preferences Model/Methods should be p-distance
Then you get the percental pairwise distances computed and plotted (0.1 means 10% differing bp/AA)
Upload your sequences to MEGA software. Then align the sequences using Clustal W option (inbuilt in MEGA). Then do the phylogenetic analyses by selecting the Phylogenetic analysis option from tab bar (Data). Another new window appears with several options on the tab bar, select the “Distance” option and estimate pair-wise distance values. Before calculating distance values , pop-up window appears, you can select different models for distance value estimation from that window.
Follow this link for MEGA software manual: http://www.megasoftware.net/manual.pdf
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